It's based on violent crime. Murders, armed robberies and the like. Felonies. A lot of the stuff you hear about in SF is more like petty crime, public nuisance, misdemeanors. But also SF is one of the wealthiest cities in the country. Rich techies aren't holding up no gas stations, even if there are a lot of homeless addicts living in tents downtown.
Either way, those sort of numbers get blown out of proportion as they relate to the average person. I lived and worked in St. Louis City - #1 with a bullet - for a decade and, while yeah there are some BAD neighborhoods, the worst thing that ever happened to me was my car got stolen (and recovered the next morning).
Anyway, South Bend is fine. The area south of campus is a lot nicer than it used to be (largely because Notre Dame has colonized it). It's probably not a "plus" for us on the recruiting front, but for most kids I'm not really sure it's the "minus" it's so often made out to be. LA and Miami are more fun, sure, but I doubt Clemson or Tuscaloosa is actually more exciting?