When I rented from SFO a few years ago, as long as you were not arriving on a flight within I think it was 48 hours, you didn't owe most of the airport tax/fees. You just make your res as "I am not arriving by plane" and it removed those charges. I don't know if that has changed in the intervening time, but you might check on it. Since you're heading south anyway, it might actually be more convenient to take BART to SFO and grab the car. Certainly don't think it will make sense to be returning the car downtown when you have a flight to catch and you're coming from the south.