They're not. People in SF act like SF streets are literally shit stained all over. In all likelihood, it's probably pretty comfortable to not wear shoes in an office haha.
I'm not sure if you're in SF or, if so, where you live/work but having lived in SOMA and the Mission, I regularly see people peeing and defecating on the street. Happened last week on the same block as Tartine, so this isn't some "bad part of town" thing either. Whole blocks regularly smell like urine. Actually this happened yesterday, I was walking right near the Asian Art Museum.
SF is not a clean city. Streets don't have to be 100% shit stained to think that maybe taking off your shoes before coming into the office is a not-so-bad idea.