For NYC, it has been estimated that every car driving in lower Manhattan incurs ... goddammit I can't find a reference so I'm going with memory here ... at least ~$3 in social costs due to increased pollution, congestion, road wear, etc.. That's in addition to the costs paid by the driver (car depreciation, gas, insurance, opportunity costs, etc.). If that memory is really true, then subsidizing transit to eliminate these social costs ends up being a huge net win!
If we want people to do something, we should subsidize it and (in the case of transit) make it free[1]. If we don't want people to do something, we should tax it (Pigouvian taxes FTW!).
[1] - Transit will never be as fast as driving due to the extra stops and walk required at either end, so we need to keep it free to minimise the total cost of fare + extra_time_wasted*salary, which corresponds to opportunity cost to riders. Riders whose total cost is too high will not ride, and riding transit is a social good (or is at least much less of a social bad then driving).