SF is safer than many of its peers, but some people seem to really want to paint the city as a failure. "Rampant crime" is one obvious way to do that. Over time the narrative leaks into the broader consciousness.

Chicago deals with the same.

I feel pretty confident that some of this is astroturfing from people with political ideologies trying to score points on blue states, but it seems to be quite effective however it is accomplished. People can be quick to scare, and appeals to their sense of personal safety are quite powerful.