Have stayed there and the Marriott Fisherman's Wharf as well as the Ren. and Marriott downtown. My favorite, although older than the Courtyard, is the Marriott at Fisherman's Wharf. You can walk to all that you can imagine in the Wharf area, Scoma's Rest. is great, as well as neat places on Pier 19. To take the Cable Cars, leave early or expect long lines, the night travel on them is supurb.
Since this is your first time one bit of advice, make sure you have plenty of warm, rainproof clothes, especially in the Summer. It is really chilly at night.
You are so right for indicating FW as a "Tourist Trap", but especially for first timers what else would you want?
There is something special about "MIxing" with fellow tourists at FW. Being able to walk, sightsee, eat and relax right around your hotel is a large plus.
In SF, the are few "Bad spots", enjoy!