Well even the buses and ferries generate revenues from fares, so they shouldn't be draining THAT much from the bridge. It would be interesting to see a detailed breakdown of where the money's coming from and where it's going to. But chances are the accountants have made it totally indecipherable.
Post #27 gives some idea where the tolls go. It looks like the mass transit is running a huge deficit, and is subsized by the bridge tolls, as I've heard reported, not read for myself. It seems that they've been reluctant to charge riders of the transit a fare that would prevent the huge deficits - their main concern is that people would just decide to drive if the fares get too high.