I believe the "farebox recovery ratio" of Muni in San Francisco is ~20%. Which means, the actual cost of a bus ride is $11.25 ($2.25/0.2). So, the government is paying $9 subsidy for each rider.
Looking at how municipalities subsidized dial-a-ride, are any subsidizing ride-sharing (uber, lyft) systems? Many uber/lyft rides inside of SF are cheaper than the cost of a muni trip.