Sure, and the same anecdotes hold in Manhattan. I've had friends robbed at knifepoint in the Upper West Side, I've seen phone jackings at 1pm in front of Gristedes in the Upper East Side. Hell, my brother's roommate in Harlem was clocked with a baseball bat in the head while leaving his apartment and subsequently robbed blind.
By and large NYC and San Francisco are both very safe cites in the grand scheme of things. (Unless you are a car window in San Francisco. Then you are screwed).
I never said San Francisco was safer than NYC, but even looking at those statistics they are mostly comparable in terms of violent crimes (notice that I did say your car is much more likely to get burgled in San Francisco), and the rate of aggravated assault is higher in that study in NYC. My point is that that both San Francisco and NYC are by and large safe cities by American city standards.
By and large NYC and San Francisco are both very safe cites in the grand scheme of things. (Unless you are a car window in San Francisco. Then you are screwed).