Following-up from Goldy's post—as someone who has lived in San Francisco for a good chunk of her adult life, there's only one thing I can say about its public transportation. It sucks. Muni sucks, the underground Muni Metro sucks, and even BART sucks (sometimes).
The only thing that's good about it is the Night Owl, which gives you an "all night special" so that you can ride for free overnight. Muni sucks even more after the service cuts. The buses almost never show up when they are supposed to—I mean you could have a frigging baby waiting for one—and good luck if you are on one of those electric lines which keeps dropping its sticks and poles.
I have missed countless birthdays, weddings, funerals, and appointments to the dentist because Muni didn't show up and spent hundreds of dollars of my meagre reporter's salary on cabs, which are equally bad. The only thing worse than a bad Muni, is a bad BART. Ever been stuck on a BART train for half-an-hour without knowing what the hell is causing the delay? Communication between BART drivers and the control room is so bad that you only get to know why the train wasn't moving when you read the news later.
The U.S. News & World Report article goes on to say that SF-Oakland were ranked low in terms of public safety. You can say that again. I was mugged by a 16-year-old on the MUNI #21 on my way to work couple of years ago—the little punk grabbed my iPhone and jumped out at a stop near SF City Hall. The entire time I was running after her, the Muni driver did nothing except stick his head out of the window and threaten to drive off with my bag and camera if I didn't get back on the bus to retrieve it.
I got to make my first citizen's arrest, but yeah, that's a good example of why Muni in general is not safe. For more examples, see video above. But as my friends in SF say, "hey, at least it's there, at least it's not Seattle."