http://www.gogonewyorkcity.com ?

That is what taxes do?
Legislators are often not in favor of the costs of transit being completely paid for by fares, because it is a disproportionate fee. It does not charge people with more money proportionality (actually charges the bottom brackets more), because they use a public system more. That is why the revenue is usually made up with a sales tax, property tax, or income tax.
Every transit system runs in the red. It is whether or not one thinks public transportation, including trains, benefits the population as a whole.

New York City transit runs at a farebox recovery ratio (a measure of fare revenues versus operating expenses) of 80 percent or higher, a figure which most transit systems do not come close to approaching. The MTA’s financial woes stem from capital debt accumulated when the system had to dig itself out of a state of near collapse caused by systematic disinvestment in the 60s and 70s. These capital expenditures were funded by debt instruments because Albany, which controls the purse strings for the MTA, refused to step up to the plate.

What’s the alternative? Twenty new bridges and tunnels for cars? New York’s highways are in no great shape either, if you’ve had occasion to drive them lately.

While $900 million is a lot, remember that the New York Metro area accounts for one-third of all transit trips in the nation. Average weekday riders total 8.5 million, and the annual MTA budget is 10.8 billion.