Rethinking MBTA weekend schedules

There is not much good that can be said about MBTA's weekend Commuter Rail schedules.

A few lines have been graced with two hour, clockface headways (Worcester, Lowell, Franklin)—not frequent, but at least predictable—but most others have service only every three hours, and sometimes less frequently. Combine that with variable headways and a lack of off-peak fares, and it's not surprising that ridership is less-than-stellar.

I suggested adding a station at Walden Pond, and today I'm going to go a step further. Rework the schedules, adding a small amount of service, to provide two-hour, clockface scheduling on all North Side lines. (I'll leave the South Side to someone else, for now, although boy could the Providence Line use better service!) A caveat: I'm not sure about how crew rules work, and that may be the cause of some of the schedule irregularities here, but we should design a schedule for passengers first, and crews can be shuffled between lines at layovers to shorten or lengthen shifts as necessary.

Newburport/Rockport is relatively easy. The current schedule works relatively well, but has some bizarre gaps. For instance, Rockport has inbound trains at 7, 10, noon and 2, and then a 3:10 gap before the next train. Going in to Boston for the afternoon? You can arrive at 3 or 6. At the beach and want to get back to the city? You can go home at 2 or 5, but not in between. Even at Salem, where the two branches interline, there is a nearly two-and-a-half hour gap between 3:20 and 5:46. For a city with a significant tourist draw (the witch museum, the PEM), poor highway access and limited parking, this schedule is severely lacking.

The two branches of the line have run times of 64 minutes (Newburyport) and 71 minutes (Rockport), so it is relatively easy to interline the two with three train sets:

This does add some service, with one extra Rockport trip and two extra Newburyport trips each day, adding about 22% to the current service. But the utility increases dramatically, with predictable train schedules and the elimination of service gaps. In terms of service hours, this schedule adds 6:38 to the schedule. The marginal operational cost per service hour, as calculated pertaining to the CapeFlyer, yields an extra cost of about $4500 per day. The line currently carries 5600 passengers on the average weekend day. Assuming an average fare of $7.50, just 600 additional riders—an increase of 11%—would cover the operational costs of these additional trains.

Fitchburg and Haverhill, however, are harder. Haverhill has a run time of 65 minutes, long enough that a single train set shuttling back and forth (see Lowell) can't make a round trip in two hours, so the current schedule has service every three hours (or so), which is hardly useful. The Fitchburg Line's current schedule is awful, with three-hour-plus service gaps and then short-turns running within a half hour of other trains.  The line is long enough that even with the new schedule accounting for higher speeds, the line would not even be able to attain two hour headways with two sets. The schedule is better than the current one, it's nowhere near clockface, with service about every 2:25, or so.

But there's no rule that says a train on the Fitchburg Line has to run the Fitchburg Line all day and all night, right? Imagine Fitchburg and Haverhill as two branches of the same line, with a train running first to Fitchburg and then to Haverhill, kind of like the Rockport and Newburyport lines. The relatively short Haverhill Line interlines well with the long Fitchburg Line, and the same three train sets can, combined, provide service every two hours on both lines.

I think that's pretty elegant. This requires just 4:12 more running time each day, or $3150 of marginal operational costs. The two lines have a combined ridership of 4500, and would require just 420 additional riders—a 10% increase—for fares to cover the costs. And the benefit would be high: the frequency of trains on the Haverhill Line would increase by 50%, from every three hours to every two.

One final idea would be to have the trains operate on a "pulse" system at North Station to enable transfers, which is attainable if every line has clockface scheduling with the same headway. Every train would arrive at a similar time, allowing passengers going from, say, Lynn to Waltham, with an easy transfer at North Station (assuming trains are on time). With the current schedules, this isn't possible. With a couple adjustments, the above schedules, with the Lowell Line, would work quite well for that.

Why is there no train station at Walden Pond?

Photo from here.

When I was hiking the Appalachian Trail through New York, I passed MetroNorth's Appalachian Trail station. Every weekend, a couple of trains stop there and drop off hikers, who can hike in either direction on the trail. There's no parking lot at the station, nor road access (although Route 22 is only a couple hundred feet away). It is scheduled specifically for hikers, and while it only serves a few hundred passengers a year, the small station is sufficient for the crowds. Breakneck Ridge is a similar station, although not on the AT, as is Manitou, although it also has very limited rush hour service.

While the Appalachian Trail was built in New York in the 1920s and 1930s (meant to serve as a regional resource for city dwellers), the Appalachian Trail station is much newer. It was built in 1991 at the behest of MetroNorth and the New York-New Jersey Trail Conference, which maintains the trail in the area. The total cost of the station? Just $10,000, with negligible additional costs for a few trains to stop. Even if only a few hundred people use the station each year, their fares add up to more than that every year.

The Bay Circuit Trail runs 200+ miles around Boston,
including around Walden Pond. Full section map here.

Which brings us to Concord, Mass. While not on the Appalachian Trail, Walden Pond is one of the most heavily-visited outdoor sites in the region, both for swimmers and beach-goers in the summer, and walkers and hikers year-round. The Fitchburg Line goes right by the pond—Thoreau rode the train there, although he may not have liked the new technology—but the nearest stations are about two miles away (Concord, which is closest, is along a busy road with a crossing of Route 2, hardly conducive to pedestrian travel). While the pond abuts the railroad, and the Bay Circuit Trail—the 200-plus mile trail around Boston—comes within a stone's throw, the trains roll through at 60 or 70 miles per hour, weekdays, and weekends.

And even if you choose to drive, Walden Pond can be hard to get to. There's an $8 per car fee, but the 300-space lot routinely fills to capacity on weekends in the summer, with a line of cars idling on Route 126, waiting for an open spot (there is minimal other parking nearby on the narrow roads in the area). And while some people certainly come by train or bicycle, many more are put off by the relatively long walk from the local train station. But what if the train stopped at Walden?

The $10,000 MetroNorth spent on its station in 1991 would be about $18,000 today, with more cost, perhaps, because the site is more remote than the Appalachian Trail Station. And two platforms might be required since the railroad there has two tracks, so the cost might be upwards of $50,000 for a simple station. (I don't know if you could get an ADA waiver given the remoteness of the station; if not a mechanical lift may suffice for infrequent wheelchair-bound visitors.) Stops could be made on weekends year-round (or at least during non-snowy months) and perhaps even on some afternoon and evening trains in the summer for late-day swimmers and picnickers.

From there, the Bay Circuit Trail provides hiking in either direction, and the station sits in the middle of one of the largest trail networks and conserved areas in the region. (We can have an argument about the merits of conservation land encouraging sprawl and high housing prices, but this at least is a large, mostly-contiguous portion.) For pond visitors, the swimming beach is a 15 minute walk along a wooded path, rather than a narrow roadway shoulder. This is about as long as the walk from Manchester-by-the-Sea to Singing Beach, at trek made by hundreds of beachgoers on warm summer days. At $15 per roundtrip, it would only take 83 passengers per day for 20 weekends of the year to make back the construction cost of the station—in one year.

Photo from here.

This could be sold as a partnership, or even partially funded through private sources. The MBTA can provide access to a DCR property and other outdoor resources. A station could even provide a safer crossing location for the tracks, which several trails cross and which now have a speed limit of 80, up from 60. It may also help tourism: the train I rode in late December had British tourists headed for Concord looking out the window at the pond, an international destination. Perhaps we should make it easier to access.

The Bay Circuit Trail, Appalachian Mountain Club and The Trustees of Reservations—two large, longstanding Boston-based outdoors advocacy organizations—could work to promote transit-friendly excursions for city dwellers. There would be more options for Walden Pond visitors to get to the reservation (and fewer cars), more revenue for the T with minimal expenses and more opportunities for people from the city who may not have a car to get outside and active. There are questions of erosion: perhaps such a partnership could put a portion of each ticket sold to and from Walden towards the maintenance of the trails there. Other than slightly longer trips for Fitchburg Line weekend riders (and given the padding currently built in to the schedule, I'm sure a stop could be built in without any delay), everyone is a winner.

This should happen.

Boston Transportation Data

Sometimes, people ask for transportation data that they assume doesn't exist but, au contraire, it does. There are some other data I have which I can provide on request, but aren't posted publicly (and some of those are based on calculations I've made which might not be entirely perfect). Here are some of the resources I know of. Most are large PDFs, because that's where data exists, right?

• Massachusetts traffic volume counts. This has most vehicular traffic counts in the Commonwealth.
• MBTA Blue Book has a lot of detailed information on MBTA operations. It does not have everything, but a lot: bus and transit ridership, some historic data (older versions of the Blue Book have data going back further; at some point I would like to compile these older data in to one document beyond Commuter Rail, which I have).
• Commuter Rail counts by train. These data are outdated (2012) but give a good idea of how many people rider specific trains, at least on the day the count was completed.
• Commuter Rail system survey. These data are even more outdated (2008) but even richer, including access and transfer data. It's pretty dense.
• Changes to MBTA service since 1964. A very comprehensive look at every bus line in the system, and every change to service in the past 50 years. 
• Summary of Commuter Rail operations, including the number of train sets required.
• MBTA salaries, in a very not-useful PDF document. I have an Excel somewhere. 
• Keolis bid document, with salary information for various positions and job descriptions.
• NTD Database, with transit system comparisons. You can also download the whole database as a database or in excel.
• Monthly data by mode, 2007-2014
• Archive of Commuter Rail schedules (Dave Weebly).

I will update this post frequently as needed. 

Go to a Public Meeting … Tonight!

In the past, this page has implored people to go to public meetings. There's one tonight that you should definitely put on your calendar:

The City of Boston and MassDOT is rebuilding the North Washington Street / Charlestown Bridge between Boston and Charlestown. It is designed with top-notch cycling and pedestrian facilities, but the designers seem to have forgotten about transit. Five bus lines cross the bridge carrying 20,000 passengers per day, including the 111 to Chelsea—a lifeline for that community—yet these riders are subject to the same delays as traffic.

There is plenty of room as the bridge is design for transit priority as it is designed, and it is most important to have a lane on the inbound side. At rush hours, 30 MBTA buses (as well as many private, last-mile shuttles) carry 1200 passengers across the bridge per hour. At the same time, the two lanes of traffic are used by about 2000 vehicles, or 1000 per lane per hour. So a lane of buses is more efficient at moving people than a lane of car traffic, even if there's only a bus every 2 minutes.

What's more, this will dramatically improve operations and reliability. Approximately 5000 people cross the bridge inbound by transit during peak hours inbound, at times when there are often five to ten minute delays. If a bus lane saves an average of five minutes of travel time on weekdays, this will amount to an annual savings of 100,000 hours for passengers on the buses serving this route. For bus operations, a five minute savings amounts to 10% of the route, which would allow 10% more riders to be carried on the same number of buses, increasing the efficiency of the route.

It's also low-hanging fruit. The entire bridge is being redesigned, so it's easy to add in a few feet necessary for a bus facility. There are no parking spaces, so there are neither impacts to the neighborhood losing parking nor issues with designing roads to accommodate bus lanes and parking spaces, one of many of the problems the Silver Line has. It should be a slam dunk. If we can't get transit priority here, how ever are we going to get it elsewhere?

The details:

6:30 PM 

The West End Museum 

150 Staniford Street 

Boston, MA 02114

We need as many people to come and speak out for transit priority as possible! See you there!

Can't make the meeting? Send public comments by Dec 25 to:

dot.feedback.highway@state.ma.us attn Project File No. 604173

or

Patricia Leavenworth, P.E., Chief Engineer, MassDOT, 10 Park Plaza, Boston, MA 02116, ATTN: Bridge Project Management, Project File No. 604173.

Saving GLX by (temporarily) cutting Fitchburg?

The Commonwealth of Massachusetts is mostly finished with a $300 million rehabilitation of the Fitchburg Line, which will yield more capacity on the line and faster speeds on the longest in-state line in the system. At the same time, the Green Line extension project has seen exponential growth in cost, mostly due to bizarre contracting methods and poor oversight. But it's still a complex project. And now an idea is being floated to cut back a branch of the line to Union Square in Somerville—a branch which parallels the Fitchburg Line—which is in dire need of better transit.

But maybe this presents an opportunity for some out-of-the-box thinking. Both branches of the GLX are slated to be built alongside existing Commuter Rail lines, and building next to an active railroad is not particularly easy. There are safety concerns, FRA issues, and even the cost of staff to insure the safety of workers—and the safe passage of trains—comes at a significant cost. If you could cut all parallel rail service, you could save a lot of time and money: rather than having to rebuild in a constrained corridor, you could more quickly build the project in a much easier work environment.

This, of course, would require cutting Commuter Rail off from the the terminal in Boston. For Lowell, this is a non-starter: busing from Winchester or West Medford would be subject to the whims of traffic on I-93, as would buses from Anderson/Woburn. And the Lowell Line also serves Amtrak and some Haverhill trains which bypass traffic on the single-tracked portions of the Haverhill Line. At busy times on this line, there is a train every ten minutes.

But for Fitchburg, this presents an opportunity. Before getting to Boston, Fitchburg Line trains stop at Porter Square. Already, between 30 and 50% of Fitchburg riders begin or end their Commuter Rail trip at Porter, transferring for a trip to Harvard, Kendall or even in to Boston. What if, for a short period of time, you closed the line inbound from Porter to allow for reconstruction, and had everyone transfer at Porter?

While this would be inconvenient for some riders, and put a bit more of a load on the Red Line, it might save a lot of time, and a lot of money, in the construction of the Union Square portion of the Green Line extension, as well as the portion near Lechmere where the branches meet and cross over the Fitchburg Line. Shuttle bus service could be provided between North Station and Porter (a 20 minute ride) but most passengers would take the Red Line. Considering that nearly half the riders already get off, and most jobs downtown are located near or south of the Red Line (in the Financial District and Back Bay) this would be only a minor inconvenience for them. With faster track speeds on the Fitchburg Line, in fact, it might actually be a wash for many commuters.

Using GTFS, I've tested out a few test trips from South Acton:

+16 minutes to North Station
42 minutes via North Station
58 minutes via Porter, Red Line and Green Line.

+6 minutes to Seaport
66 minutes via North Station and #4 bus
72 minutes via Porter, Red Line and Silver Line

+5 minutes to Copley
56 minutes via North Station and Green Line
61 minutes via Porter, Red Line and Green Line

+3 minutes to Park Street
52 minutes via North Station and Green Line
55 minutes via Porter and Red Line

0 minutes to LMA
72 minutes via North Station and Green Line
72 minutes via Porter, Red Line and #47 bus

0 minutes to South Station, Kendall and Harvard
58, 48 and 42 minutes via Porter already faster than via North Station

It's a wash for most commuters other than those traveling to North Station, and most commuters' final destination is not at North Station, but somewhere to the south (since North Station is mostly surrounded by highway ramps and water). In the long run, running trains to North Station makes sense. But if service could be curtailed at Porter for a year to save millions of dollars, I think it is a worthy sacrifice.

In addition, service on the Fitchburg Line could increase in frequency. Each train terminating at Porter would save 20 minutes of round trip running time. This could be translated in to an extra trip in each rush hour to help spread the load, and an extra midday and evening trip as well using the same equipment. It would also be a good opportunity to, once and for all, construct high-level boarding platforms at Porter to allow faster boarding of trains at the station. The two-track station would be more than adequate for the current schedule on the Fitchburg Line, and during the midday, trains could be stored on the tracks beyond the station well shy of construction in Union Square.

The five train sets currently stored in Fitchburg would be enough for full service on the line; the first train arrives in Porter at 6:40 and could easily make the outbound run to Littleton for the 8:20 service back to Boston in the morning. In the evening, the first outbound train to Littleton could easily turn back to Boston in time for the late local departure at 6:20 (which could be pushed back a few minutes with no ill effect on passengers).

With the route mostly cut off from the network, light maintenance would have to be established somewhere along the line (perhaps at the maintenance of way facility near Alewife). For heavier maintenance, trains would have to be shuttled to Lowell across the Stony Brook line from the Willows. This railroad is slow and would need improvement for anything but occasional moves (if it were faster, it could host passenger service from Fitchburg to Boston via Lowell) but would likely be adequate for short-term moves. The extra crew costs would be offset by the savings of rebuilding the inner part of the line quickly and economically.

Is there precedence for this? There is. From 1979 to 1987, the Southwest Corridor was rebuilt below grade between Hyde Park and Back Bay for the relocated Orange Line. The issue was that the Needham Line was only accessible via the corridor. Rather than keeping a track in service and continually moving it around for the rest of the rebuild, they shut down Needham service, replaced it with express buses (which encountered less traffic on the Turnpike than they would today) and rebuilt the corridor in place, That project is obviously larger than the Fitchburg project, and necessitated a longer shutdown, but there are certainly similarities which could yield similar cost savings. See page 202 here.

The "Profitable" CapeFlyer: Innovation? Or Accounting?

When a teenager borrows his parent's car for a cruise around town, he assumes that driving is cheap. He drives 20 miles, put a dollar's worth of gas in the tank, and voila, it only costs 5¢ per mile. Never mind that mom and dad plunked down $20,000 for the car, paid sales and excise taxes, and take it in for maintenance (and probably pay for the increased insurance cost that come from having an inexperienced driver as well). Those are all fixed costs, whether Junior drives it or not. Junior only pays the marginal cost of driving—a few cents per mile—which is a small percent of the actual cost of owning and operating a car, so to him, it seems pretty cheap.

The Frontier Institute makes exactly this point in a recent blog post (I even get a mention!). Now lets extend this logic to the recent, inaccurate report that the CapeFlyer train makes a "profit", while weekend Commuter Rail service operates at such a loss that the MBTA Fiscal Control Board wants to cut it. The Control Board unfairly compares the two services, using the same “logic” that makes Junior think that driving is a great bargain.

If someone else pays for every aspect of driving except for the gas, then, yes, driving seems cheap. If someone else pays for the all of the fixed costs of operating a passenger rail service except for the crew and the fuel—as is the case with CapeFlyer—it seems cheap as well. Comparing CapeFlyer's marginal costs against the overall cost of Commuter Rail is as silly as saying that a teenager's topping up the tank of their parents' car pays the entire cost of car ownership.Yet that's exactly what the MBTA Control Board does in claiming that the "innovative" CapeFlyer is a model for weekend Commuter Rail funding. It's not.

A bit of background: in 2013 MassDOT and the MBTA started running the long-overdue CapeFlyer service from Boston to Hyannis (in about 2:20, just 35 minutes slower than 1952!). The train makes three round trips per week, one each on Friday, Saturday and Sunday, from Memorial Day to Labor Day. It has decent ridership—nearly 1000 per weekend—which is not bad given its limited schedule. And according to every published report, it turns a profit.

Wait, what? A train turns a profit three years in a row? If it's that easy to turn a profit, then we should have Commuter Rail popping up all over the place, right? Private companies should be clamoring to run trains every which way. If it is profitable to run a few round trips a week to the Cape (with mostly-empty trains back; I can't imagine there are a lot of Cape Codders coming back to Boston on a Friday evening), then surely full rush hour trains—some carrying upwards of 1000 passengers—must make a mint for the MBTA.

Of course, the reason the CapeFlyer makes a profit is because its finances are accounted for very differently than the rest of the MBTA: it makes a profit against its marginal operating costs, but this misleading calculation does not account for the significant fixed costs that come from running a railroad. There’s nothing wrong with this – the CapeFlyer runs on the weekend and uses equipment, crews and trackage which would otherwise sit idle. It’s a good idea to offer people more rail options. That’s not the issue.

The issue is that when the MBTA Control Board proposes cutting Commuter Rail weekend service, they compare that service against the CapeFlyer, without accounting for the fixed costs that CapeFlyer doesn’t have to worry about. If we analyze the cost of weekend Commuter Rail service the same way we analyze the cost of CapeFlyer service, the Commuter Rail service would look a whole lot cheaper than the T’s Control Board makes it out to be. But when the preconceived agenda is to cut service, a fair comparison quickly becomes an inconvenient comparison, and therefore they resort to the accounting equivalent of comparing apples with oranges.

Let's do some math.

The CapeFlyer runs 15 to 16 (16 in 2015) weekends a year, plus extra runs on Memorial Day, July 4 (sometimes) and Labor Day. That's a total of 47 to 51 days—let's say 50 for the roundness of the number. The distance from Boston to Hyannis is 79.2 miles (about 80), and it makes a round trip each day, so the total distance traveled is about 8000 miles. The operating costs are about $180,000, yielding an overall operating cost of $22.50 per train mile (or about $750 per train hour; note also that a Northern New England Intercity Rail Initiative report had very similar operating costs for a five-car Commuter Rail consist: $22.97 per train mile or $793 per train hour). Just the cost of the crew's hourly wages and fuel adds up to about $150,000 [1]. If you ignore all the other costs of running the railroad (capital costs and depreciation, vehicle maintenance, maintenance facilities, stations, signals, crew benefits, maintenance of way, overhead costs, etc.) then, yes, the CapeFlyer makes a profit.

This graphic contains a footnote which reads:
"Average cost, including an allocation of fixed costs 
which may not vary if service is reduced."

In other words, the report even goes so far as
to admit that most of the costs of operating
Commuter Rail are fixed costs, by a 3:1 margin.
Note how they bury this slightly important
information deep in a footnote that no one is
going to read.

But what are the actual costs? According to the National Transit Database, in 2013, the T's commuter rail operated at a cost of $15.92 per vehicle revenue mile. Not train revenue mile. Vehicle revenue mile. The Cape Flyer is generally made up of nine vehicles: eight coaches and an engine (often two for redundancy; a rescue train would be hours away from Hyannis). So the actual cost of the CapeFlyer is $15.92 times 9: $143 per mile. That's more than six times the direct marginal operational costs which are used to show the "profit" that the train apparently turns.

If the CapeFlyer had to cover all of the fixed costs as well as the marginal ones, it would be bleeding red ink, just like weekend Commuter Rail service.

And there's the rub. The MBTA Control Board wants to nix MBTA Commuter Rail service, because they ascribe to that service the full costs of running the trains, while pointing to the CapeFlyer as an example of a "profitable" service when it comes nowhere near to covering the costs that weekend Commuter Rail is asked to cover. It is not a fair or principled comparison.

Most of the costs in running weekend Commuter Rail are fixed. The Control Board even admits this (see the screenshot from their report to the right). We already have the trains. We already have the stations. And the track, and the signals, and the crew benefits and all else. According to the Control Board documents, the average weekend subsidy per ride is $23.52. Assuming the average fare paid is in the $6 range, fares cover only 20% of the costs of running the trains on the weekends (overall, fares pay about 50% of the cost of Commuter Rail). But let's assume that weekend Commuter Rail trains are accounted for at the rate of the CapeFlyer: $22.50 per train mile [2]. If we only count those costs, the total cost per passenger drops from $29.52 to between $4.52 and $10.33 [3]. That's a lot less than $30, and in some cases, less then the average fare. So, using the same "innovations" that the CapeFlyer uses to turn a profit, weekend Commuter Rail service might well be able to turn a profit, too. Even if you assume that weekend service would use shorter trains (and therefore cost less) it would certainly require less than a $30 subsidy for each passenger. [4]

By not accounting for the fixed costs, CapeFlyer appears three to seven times cheaper to operate than regular Commuter Rail service. But perhaps instead of using these numbers to kill weekend Commuter Rail, we should use them to enhance it. If the CapeFlyer can show a profit at an operating cost of $22.50 per train mile, better Commuter Rail service on other lines likely could as well. Right now, with high fares and infrequent, inconvenient service (on some lines, only once every three hours!), weekend Commuter Rail ridership is low. What if we had hourly service (and perhaps lower off-peak fares) to and from Gateway Cities like Lowell, Worcester, Lawrence and Brockton? What about convenient, hourly service from Providence to Boston (which is generally faster than driving), with tourist attractions at either end of the line. And certainly hourly service to the beaches on the Newburyport and Rockport lines; lines which often fill trains in the summertime, despite the anemic current schedule.

We already pay for the track, the stations, the signals and myriad fixed overhead costs. The marginal cost of running the trains themselves—as the CapeFlyer shows—is relatively low. If we apply the accounting "innovation" of the CapeFlyer to weekend Commuter Rail service, it would be an argument to run more service, not less. If we're going to uphold the costs of Commuter Rail with the CapeFlyer, perhaps we should try that.

A note before the footnote calculations:

While CapeFlyer has a higher fare than any other Commuter Rail service, it is not really a "premium service." The $22 fare for 79.2 miles works out to 28¢ per mile (cpm). For comparison, the 49.5 mile trip from Fitchburg to Boston costs 10.50 (21 cpm), but shorter trips cost a lot more—some coming in at double the cost per mile of the Cape Flyer. So higher fares do not come anywhere close to account for the difference between the "profitable" CapeFlyer and other services. There are savings available for monthly pass-holders, but this is only in the range of about 20%. Even with these discounts, any trip inside Zone 6—approximately I-495—is more expensive than the CapeFlyer.

From Keolis bid documents. 3/4 of the cost categories are fixed costs.
As is some of the fourth.

[1] This assumes 4 crew members for 8 hours including report time and layover time per day, 50 days of operation. $43/hr for an engineer, $35 for a conductor, $34 for each of two Assistant Conductors. Total direct wages of $58,476. See page 10 here for exact numbers, and note that there are a lot of other staff listed there beyond these which are not included in the calculation (nor are benefits, which account for an additional 40% of pay, but are fixed costs). A Commuter Rail train uses approximately 3 gallons of diesel per mile of operation, so 8000 train miles per year use about 24,000 gallons of diesel. Diesel prices have ranged in the past three years from $2.50 to $4 per gallon, for a cost of $60,000 to $96,000. Thus, the total crew and fuel costs range from about $120,000 to about $160,000.

[2] And, no, comparing hourly costs does not make this any different: the CapeFlyer and regular weekend Commuter Rail service both average about 35 mph.

[3] $4.52 if you compare a nine-car train like the CapeFlyer, $7.67 for a five-car train, and $10.33 according to the Control Boards own documents comparing the net marginal costs and the total costs. In theory the T should only be reporting costs for open cars during operation, but that doesn't seem to be the case.

[4] Let's look at this another way. A train from Boston to Worcester runs 44.5 miles. At $22.50 per hour, that means it's direct CapeFlyer-accounting costs is almost exactly $1000. If the cost per passenger is actually $30, it would mean that only 33 people were on the average weekend train. I have taken the Worcester weekend service many times, including the (at the time) 7:00 a.m. outbound train. And there were quite a few more than 33 people on the early train outbound from Boston (more than I expected). The average weekend train carries about 100 passengers per train according to the report's numbers, closer to 150 per train according to the T's data (although ridership has dropped in recent years, perhaps owing to more elasticity on weekends when the train is less convenient and parking costs are lower). For what it's worth, a CapeFlyer train only carries, on average, 130 passengers.

Finally, the T pays Keolis $337 million each year to run Commuter Rail on average—$308 million in 2015—and trains run approximately 4 million miles per year and 22 million coach miles per year. This works out to an average train length of 5.5 cars (about right), a cost per coach mile of $15 (about right) and a total cost of $84 per train mile—about four times what the "profitable" CapeFlyer costs, and that's at the low end of the estimates.