>I haven't read of a public transit system where the fares covered the costs of building and operating it. I have read that MTA (NYC), BART(SF), Amtrak[1], NJTransit, and other US ones definitely are in the red year after year.

In all of those cases, the fares plus gain in property values far exceed their costs. Indeed, every one of those authorities realizes that it would be net money loser on the sales/property/business taxes generated if they could stop paying maintenance and shut down the transit systems for free.

[1] Edit: except maybe that one.