San Francisco commercial corridors do not allow chain retailers as a measure to preserve neigboorhood character. As a side effect this somewhat keeps the rent down. One of the few examples where over regulating a market kind of works well..
Chipotle wanted to open a restaurant in the Lower Haight right next to the MUNI station; it got voted down, and it was no particular loss to me since the Mexican restaurants around there were far better anyway, but that location was empty when I moved there and only now, 6 years after the original business closed is it being torn down to build apartments.
And I don't think anyone is claiming commercial rents in SF are cheap; the best you could say is "maybe it would be worse if we removed this one rule and kept all the others"
http://sfist.com/2017/05/15/blue_bottle_blocked_from_opening...