> On top of that, it is horribly inefficient to have people commute 40 miles (~64 km) to their office. There is certainly some animosity towards these kinds of commuters who often spend very little time actually in San Francisco, pay little to no city taxes, but want to live here.

This is arguable. Those people probably live in SF because they want to spend their evenings and weekends in the city, therefore spending all their money there (including on basic living expenses, like groceries). Most people don't really spend any money during work hours (except maybe for lunch, but that's a moot point when talking about Google/Apple/Facebook).

Also, the two city taxes I can think of are property taxes (which are rolled into rents anyway) and sales taxes (which are paid whenever they buy something inside the city). I don't see how commuters don't pay city taxes.