We were having our reception nearby at the Fort Mason Golden Gate Room so were looking for a nice, non-denominational location to have the ceremony. We could not have been happier with the Chapel. It is a cute, relatively simple, but still beautiful space with nice pews and some nice stained window details. There is a helpful little room at the entrance for bride, etc. to get ready (although I didn't actually end up using the room). Parking for the guests was no problem, and it was a beautiful quick walk down to the Golden Gate room. James Sword (who handles the reservations, etc.) was very nice and flexible, especially when I had some trouble getting the required event insurance and ended up missing the deadline. Price includes 3 hours for the event (which was fine for set up and take down and a 40 minute or so ceremony) and a rehearsal (if scheduled during normal business hours) which we didn't end up doing. Only thing to consider is that you do need to have everything out of the chapel by the end of your rental time, but we managed relying on the help of our friends to clear out the flowers and anything else left inside.
All in all, we were extremely happy with the chapel and its location. Price was reasonable considering what many places charge for wedding related events.