It's just so easy to get a car in SF whenever you need it for a few bucks -- sometimes in 15 minute increments.
1. Caltrain which connects downtown SF to San Jose and Gilroy, notably bypassing both SFO and SJC airport [1]. This is a low frequency, mid-long distance commuter rail link that runs almost exclusively outside SF.
2. BART which connects SF to the East Bay, notably serving both SFO and OAK [2]. This is a medium frequency, larger train - think a hybrid of commuter and light rail. It's fast, long trains that run medium distances.
3. Muni Metro which is the SF subway and light-rail service. In the downtown corridor, all the major stations (from Civic Center to the Embarcadero) overlap with BART, but the trains continue out west into the Sunset [3]. This is high-ish frequency, smaller trains that (outside the downtown corridor) run overland.
[1] http://www.caltrain.com/stations/systemmap.html
I don't think I'm going to take public transit in San Francisco ever again. They are missing:
* Speed - BART is relatively fast, all Muni is very slow
* Frequency - BART is low frequency, Muni is also low frequency
* Coverage - BART coverage in SF is limited, Muni coverage is reasonably extensive
* Reliability - BART unannounced delays and breakdowns were a frequent occurrence. Unlike Tube delays (which were also frequent) I could not route alternatively because there is only one BART tube in SF. Muni does not have arrival times.
* Usability - You cannot tell before you pass the turnstiles at a BART station whether the lines are delayed or when they will arrive. One exception I know if is Montgomery St. Station but that's the only one.