In SF it really depends on which line you're on, and a bit of luck. In my experience the 9 was the worst. I didn't ride that one often, but almost every time I encountered something ridiculous. One time a guy rolled a blunt and started smoking it on the bus. Another time a guy in a wheelchair spilled a bottle of booze that then ran up and down the floor of the bus. I got off early several times when an obviously crazy homeless person got on and started silently staring me down.

But even popular commuter routes like the 38 can get pretty dicey. One time a guy was blasting music out of a bluetooth speaker. He had headphones sitting on his neck, so I asked him to use his headphones instead. His response was to get in my face and start yelling, threatening to beat me up. Everyone around us stepped away and ignored us. Apparently the next stop was his, so he got off while threatening to jump me if he ever saw me again.

If you take public transit in the bay area regularly, you are almost guaranteed to have some very unpleasant experiences.