Here in Denver, the public transportation is heavily subsidized by sales taxes. Depending on whose statistics you listen to, 20-40% of the cost of running RTD comes from farebox revenue (the rest comes from mostly a sales tax levy and some from federal grants). City route buses get about 4mpg, and they use so much fuel that every 1/10 of a cent rise in diesel comes out to $100,000 annually.
The worst waste is required by ADA. AccessiRide (those short buses for the severly handicapped) cost RTD about $45 per trip.
Subsidizing public transport isn't necessarily bad - if there were no buses how much sales tax would it cost to build enough bridges/freeways/parking-lots etc so that everybody could drive into downtown. What about in Manhattan?
The point was that it is one of those areas were making cuts to save money gets counter productive very fast.
OK we will cut routes, put up fares, reduce number of trains/buses.
So there are now fewer people wanting to use the more expensive overcrowded unreliable service, OK we will have to make more cuts.
Eventualy you aren't actually running any trains but are still paying for all the fixed cost infrastructure.