I was in San Francisco a couple of times back in January, but I was too darn sore from my surgery to go club hopping. The friends who were with me did take me over into the Tenderloin area, and I did see MtF folks out and about, although several looked like "working girls". There are clubs and restaurants that I was assured would be safe there, but I cannot say specifically which ones they are.
On the other side, I and my friends had NO problems anywhere we went, on the days before the surgery, when I could walk comfortably, the Embarcadero area was a lot of fun just to visit.