It has to be said, SuperShuttle and similar services work VERY well from/to SFO, all things considered. It's sometimes a bit of a drag to use them when you're catching a 6am flight and they come 15 minutes early to bundle up different passengers on route to the airport, but otherwise the local geography lends itself very well to these services.
Also worth keeping in mind that BART (local Metro service) does basically a door to door from inside the international terminal to the Powell Street station on Market, two blocks from Union Square, for just over five dollars. Depending on the time of day, just to avoid the traffic, I'd look into that.