The $30 billion I spoke about earlier is only a small piece of a massive amount of subsidy necessary to maintain roads and highways. If gas tax revenue is devoted entirely to highway maintenance, then what money goes to mitigating gasoline externalities and pollution? And don't forget about non-interstates, either. They are 97.5% of roads.
There was a hugely comprehensive study on this last year, actually, which covers this in way more detail than I have energy for: Do Roads Pay For Themselves?
I also would prefer to see the Big Dig and other roads funded by tolls, at least to a much larger extent. Certainly that would be more fair to I-90 users. Note that the TFC identified a funding gap for the Western Turnpike as well as the Boston extension, though.
MBTA's budget is $1.62 billion. Of that, $405 million is due to debt service, not operations cost. Of the $1.2 billion remaining, about $300 million goes to the Commuter Rail subsidy. $400 million to wages. Notably, the RIDE costs about $84 million, but should really be considered a state aide service that for historical/arbitrary reasons is provided by the T.
The method of counting cost per user is not a bad one for purposes of analysis, but it is far more complicated than what you have presented. Marginal operating cost per rider for the T is negligible and goes down the more people ride it. Increasing the number of vehicles commuting into the city of Boston increases the operating costs of the roads, and accommodating all those cars costs the city tremendously in terms of pollution, space on the road and parking lots. The T has lots of problems, but the city couldn't function without it.
I should probably clarify, that I'm not pro-car unless it makes sense-- there's no kind of transit that can effectively serve anywhere built after WWII, (128, 495) but where areas were built before WWII, transit should be put into place. I'd love to see real high-speed rail going to areas that it makes sense and provides a real time advantage over a car. If I lived in say, woburn, and drove to Boston it would probably take an hour door to door, but if I took the train it would take a lot longer-- get to the station, wait for the train, take the train to north station-- then walk or take the T to my job. The timing gets even worse for the commuters that are further out-- so they don't even consider living close to the city and the sprawl gets pushed out to Leominster and Fitchburg.
Being in Boston, it's easy to forget, but 90% of Americans drive to work. Building transit out to single family homes and two story apartments in an area like Columbus or St Louis makes absolutely no sense.