A couple months ago, the Federal Transit Administration  updated its National Transit Database  to include data from 2011. Their database analyzes the country's major public transit systems in many ways, including by size, usage, and budget.
The NTD includes "Fare Recovery Ratios" for transit systems across the USA. This is the percentage that passengers pay - out of pocket - compared to what their rides actually cost.
The data is further broken down by system and within each, by mode of transportation - so, subway (light rail and heavy rail), but also commuter rail, bus, an boat rides.
Passengers in Boston and in Massachusetts pay wildly different percentages of real costs. (The data is from 2011, prior to the July 2012 fare increases.)
Heavy rail transit riders (Red Line, Blue Line, Orange Line) pay about half of what their rides actually cost, as do light rail users (Green Line). Commuter rail passengers pay about 44% of the cost of their rides.
Demand response users (which I believe means "The Ride", here in Boston) pay just 4.14% of the cost of their rides.
The MBTA reports this information , too (Page 12). Although it's from 2009, the report I found details how the T compares to other major US transit systems when it comes to cost recovery.
Heavy rail users in Massachusetts appear to be paying just a bit more than riders in other states, at almost 54%, but light rail users are getting smacked, paying the highest percentage among six major metropolises. Ferry boat riders cover more than 60% of the cost of their rides, far and away the highest percentage, nationwide.