Mass transit is subsidized, in most cases, FAR beyond whatever the externalities cost.
In Boston, 75% of the cost of each fair is payed for by other taxpayers. I dated a woman getting her PhD at MIT in transportation studies for a few years and asked her "are there any studies showing that the negative externalities that are dealt with here cost anything like the MBTA subsidy?"
The answer is no - even if you count externalities, most public transit is a huge exercise in value destruction.
I lived in Boston for a summer in 2006, and I got to witness the transition from decades-old transit tokens to paper cards.
It was a giant cluster: Horrid machine usability, non-reusable transit cards, and untrained station personnel. It made me wonder what sort of premium the MBTA paid for that "upgrade" and how much rider confidence was lost.
So anyways, they're about 30 billion in the hole over the next 10 years for what it will cost to do routine maintenance on the system going forward, mostly because it was all neglected for 20 years during the big dig fiasco.
I continually wonder why we can't build these things in this country anymore.. in the 20th century, a whole bunch of cities went from 0 to a complete transit infrastructure. These days, adding a single line or extension is a multi-decade fiasco (green line extension in Somerville, or the second east side line in manhattan).
Why is it that the MBTA, BART, the Phoenix light rail, etc. always have these problems (unrealistic projections, turf battles, overlapping spheres of control, etc.), and yet Greyhound, Southwest Airlines, etc., don't?
I'd suggest that this sort of problem is endemic to government run transit organizations, and doesn't crop up in the private sector because there's competition, and private firms can only get as many dollars of budget as the paying public is willing to give them.
Horrific incompetence results in extinction ... in the private sector.
The same oughta be true when evaluating different methods of solving other problems as well. Busses can be run by private companies as long as the government provides the roads, because you don't need government involvement to drive on a road.
Building a road, or a train track, requires some amount of government involvement, especially in dense areas with small lot sizes. Unless we're gonna knock down half the skyskrapers for 30 story parking garages in our major cities, we need to find a way to make mass transit work.
There's 2 approaches towards that -- try to help the right people get into government, or throw your hands up, bury your head in the sand and declare that "databases are never the right solution".
Most cities wouldn't be able to function if you hard to park a car for every workday commuter. Especially Boston, I used to live there, you telling me there's room between the South End and Beacon Hill for all the people that work there? Maybe if you paved the commons and turned it into a 5-level garage. Sounds lovely. And that's not even getting into what it costs to pay welfare and housing for all the people who would no longer be able to hold a job without a way to get there (not as big a deal in Boston since the subway barely goes to Dot and Roxbury as it is - they're on the bus anyways).