I stayed downtown San Fran, at the Whitcomb Hotel as it was walking distance to the Opera House. Every San Fran native said to stay by Fisherman’s Wharf. I personally wouldn’t stay downtown again. There are a lot of mental health patients out in the day and they do drugs and smoke up right on the grass in front of the government buildings. I am used to this sort of stuff growing up downtown Toronto, but the difference is they are so high they will come so close to you to talk as they have no conception of personal space. On a good note, at night the police is out in full force and there are no homeless people or druggies out, but by the morning they are all there again – it was the oddest thing!
I have family members who always stay in the Fisherman Wharf's area, and there are several national chains there with good rates. But there is a pervasive fishy smell in that area. You also have the problem of derelicts on the sidewalk that can be scary after dark. And this would be a long cab ride after the performance.
I much prefer anything in the immediate area of Union Square. There are several major chains, as well as boutique hotels. If you shop around a bit and look for their AAA rates, prices aren't so bad. (I've never tried the Inn at the Opera, but might look into that in the future.) You need to take a cab back, but it's half the distance of Fisherman's Wharf. During the day, you are right on the cable car line, which is always fun.