There are some hotels in SF that include parking charges although rare. We found a few in the Lombard/Gough street area and stayed at the Buens Vista Motor Inn, it was nice but it was also a few years ago so you should check out current reviews. From there it was quite an easy walk to Fishermans Wharf and transport into the city centre.
I prefer the San Remo, but you have to park down the street at the Safeway overnight. The Holiday Inn used to not charge for parking, but it's been a few years since I've stayed there.