2 years ago 4 of my friends at Sega got mugged the day they arrived in San Francisco for the Game Devlepers Conference. One of them got a broken tooth and a concussion.
I don't know San Francisco that well yet but in the interest of trying to prevent something like that happening again here's a map.
Consider the red areas places my best guess at places you should not go. That doesn't mean you shouldn't be careful everywhere but those areas in particular seem more dangerous.