This is truly a lovely little place. Although it's the apartment under a main one, it still has a really nice, homely feel to it. Hosts John & Sue were a pleasure to deal with and REALLY helpful!! It was clean and tidy and the pull out sofa was pretty comfy, not perfect, but good enough!! We didn't explore public transport, but there were buses nearby. Also about a 20/25 min walk from AT & T Park if you're heading to the baseball. It's well away from Fisherman's Wharf though. We did the City Sightseeing bus which dropped us about a 8 min walk from the nearest stop, so that's an option.
My only criticism would be the noise issue coming from the apartment directly above us. Whilst this is no relection on the hosts, the people there at the time were noisy and we heard most conversations and footsteps, so it was pretty annoying. But other than that, I would highly recommend this apartment for a short stay - but do your research on where you want to go and how you're going to get there prior to your stay! 9 out of 10!