Having lived in SF for a while now, I've found this to be true about the transportation:
1) Subway (Bart) is a joke. It makes one slash across the city. If your destination isn't near the slash, you have to cab or bus.
2) The bus system works okay once you hold your nose and take the leap.
3) I don't know what people are talking about in terms of dirty cabs. The problem is finding them. It can be the most annoying part of a day; you're late, you want a cab, and you literally can't buy a ride. If it's raining forget about it. Forget about everything--you're not going anywhere.
Other than that it's an incredibly beautiful city.