For example, SF MTA is part of the SF budget, but LA MTA is a county agency, and isn't part of the LA city budget.
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.
Their per capita budget is half of SF's.
True, but most likely in a way that also reduced the cost in other cities and counties, because the high cost of SF has pushed people out to lower cost areas in the outskirts. If SF wasn't so expensive, more people from the surrounding area would live there, having the desire if price wasn't the issue, therefore reducing demand and thus costs for the outer areas.
Even if the money was burned that would be okay.