That has nothing to do with it, at least for me. When I am in San Francisco for meetings, I am usually staying near Embarcadero because I can walk to meetings. The hotel is right next to a bunch of office towers where I usually have meetings. Plus I like going over to the Ferry Terminal. If am there for a conference, I usually stay near Union Square as conferences are typically nearer there (either at Moscone or at a hotel like Marriott Marquis). This goes for hotels really in any city, I stay where I can walk to where I need to be.

Union Square can have its issues, but I have stayed at hotels near there without incident and have had good stays, I plan to stay in Union Square the next couple of times I am in the city (again due to location in terms of where I need to be).

EDIT - With that being said, if I am in SF for a leisure stay, I would probably end up near the Embarcadero versus Union Square.