I have always been a fan of the
JDV hotels. I have stayed at the Phoenix and the Hotel Carlton. They also have some hotels in the east bay.
The Phoenix has free parking, and the Hotel Carlton has a lot that you can pay for and leave your car. (somewhere like $30 a day)
As Alex said, the good and bad areas are intermingled when you are in the city. One just needs to be aware when walking. I have never had a problem and I have walked all over the place at all hours of the night.