Rental car prices are historically better ON AIRPORT. If you are already in San Francisco, my hint for a cheaper ride to pick up the rental car is to reserve a shuttle TO THE AIRPORT vs. POINT TO POINT (for example from our hotel near Golden Gate Park to the McDonnell Drive car rental location it was $25 cheaper with my method).
When making the reservation, I chose a time that would get us to the airport 30 + minutes prior to rental car reservation (and good thing! there was a huge line and it took us 30 min to get waited on).
I stated our drop off at the airport as "Departure from Terminal 3" and just picked a random airline. When dropped off at the Terminal, we simply went inside, took the escalator up to the AirTrain, and rode to the Car Rental center. Easy-peesy and cheaper!

I'm surprised, but glad this worked for you. Most airports have such high additional taxes/surcharges that it is usually much cheaper to rent from a location off the airport. Throw in a couple of shuttle or train tickets, and you'd be losing even more!

But this shows how you can save by shopping around- including alternate locations- then verify all the details and other costs (such as transportation and time) to get the best deal.

San Francisco car rental rates are almost always MUCH higher at the airport; I think this was an anomaly.

>>Rental car prices are historically better ON AIRPORT

I humbly rescind this post, i am obviously uninformed...

You might want to use Kemwel or Autoeurope to compare prices. Specify the pickup and return location and see if there is a price differential between the SFO pickup and the downtown pickup.