"Fares bring in a lot of money, but they cost money to collect—6% of the MTA's budget, according to a 2007 report in New York magazine. Fare boxes and turnstiles have to be maintained; buses idle while waiting for passengers to pay up, wasting fuel; and everyone loses time," explains The Economist's Gulliver blog. One idea, floated recently by Slate blogger Matt Yglesias, would be to implement proof-of-payment systems instead.
However, "[p]roof-of-payment systems don't solve the problem of fare-collection costs as they require inspectors and other staff to handle enforcement, paperwork and payment processing," says The Economist. "Making buses and subways free, on the other hand, would increase passenger numbers, opening up space on the streets for essential traffic and saving time by reducing road congestion."