First off, if you haven't booked your flight already, you should consider flying into Oakland rather than SFO. Slightly closer to Santa Rosa, but more importantly traffic is generally significantly better than from SFO because you don't have to drive through SF.
Since I live here I don't really have any hotel recommendations--depends on what you want to see and do while you're here. I've played at the Embassy Suites, and it seems like a nice place, and is well located as mentioned. You could be in SF or SR in 30 minutes unless you go during commute hours in commute direction (south in the AM, north in the PM).