Are Hong Kong, Seoul, Tokyo, Singapore all massively subsidizing their mass transit? Do they have enough riders that they're profitable? Are they more or less efficient in how the manage them?
How about Amsterdam, Copenhagen, Stockholm, Antwerp, Koln, Barcelona, etc... which are all an order of magnitude smaller than the previously mentioned cities but all have pretty good public transportation.
These last cities are all on the same order of size as SF. About 1 million people each and yet they have vastly better public transportation than SF