Seems like a fair comparison to make would be with NYC, whose city government similarly subsumes the counties/boroughs. NYC's per capita budget is about 2/3 of SF's; there may be economies of scale and other non-linear contributors at play with NYC's 10x larger population, or maybe SF is just less efficient.

edit: NYC's MTA is funded separately, including huge state contributions, so this is a terrible comparison. Let this comment be a reminder of the difficulty in comparing municipal budgets.