San Diego Zoo leaves a lot to be desired. Half a day is plenty and unless you are a huge fan of zoos, just skip it.
I would including Liberty Station. close to the airport. some nice shops and great places to eat.
Instead of the Zoo I would spend a few hours walking around Balboa Park.
agree with everybody NOT to rent a car while in SF. Most hotels will charge $ 60+ a night to garage the car + you don't want to drive in SF.