I lived in SF for years, and I don't ever remember seeing its flag... although the motto (Oro en paz, fierro en guerra -- Gold in Peace, Iron in War) is common (e.g. on Police badges), I kind of liked that it was in Spanish too.
Yeah, if you're looking for it, you can see the phoenix motif all around San Francisco, not just on flags. It's the symbol of the city.. a city risen from its ashes. I quite like it actually, though I agree the actual flag is not the greatest design. He didnt mention it but the gold border is a reference to the gold rush roots of the city, if that wasnt apparent.
I dont think the flag is that hard to find.. it's flying over most government buildings at least. Though I may be inclined to notice these things since I could name the cities for a few of flags on his "bad flag" slide by sight.
https://en.wikipedia.org/wiki/File:Flag_of_San_Francisco.svg