If you're looking for a really nice and quiet place to stay for an affordable cost - Stay with Cami and her family. She allowed me to come and drop my bags off early the day I flew in and also let me leave my bags in their home while I explored the city before my red-eye flight. We didn't interact much while I was there due to the fact I was at a conference during the day.
Things to note: You'll be sharing your basement space with two additional rooms which might have 2 people in them so wake up early to use the bathroom/shower. I had to time my showers just right, but besides that there wasn't much of a problem. Also bring flip flops because the bathroom gets VERY wet from other visitors.
Also if you're concerned about getting into San Francisco without a car - The BART is a safe 10-15 minute walk from the house.