Aloha, We will be in San Francisco the first week in October for three days,we need a car for the second and third day as we will drive to Pt.Reyes Station.We were told to catch a shuttle to our hotel and than get the shuttle back to the airport on the second day to get the car, the shuttle will be $14.50 per person.Is it just better to get the car when we arrive?It will be our first time driving in CA.Any advice will be greatly appreciated.Pakepf3

I'm trying to figure out the benefit of going clear back to the airport to get a car on your second day and paying $29 to do it. You may have to pay for overnight parking in SF for one night, but I would't want to give up that three or more hours of going back out and getting the car, etc.
The other option is checking on picking up the car in the city somewhere convenient to your hotel which may or may not actually be cheaper than getting one at the airport.

Hertz Avis and National all have locations for pickup right in downtown San Francisco, probably walking distance from your hotel...if not, some of them will pick you up and drop you off. I can tell you the most convenient for pickup if you post the neighborhood of your hotel.

P.S.
When you first arrive at SFO, it may be necessary to take a shuttle to your hotel if you have heavy luggage and your hotel is not near a subway station. But to get back to the airport with no luggage, pay $4.95, not $14.50, by taking the BART.

www.bart.gov/guide/airport/airport.asp

I'd take a shuttle or BART into SF and then rent a car from a rental location in SF itself as others have mentioned. This will save you time and money.

I can tell you the most convenient for pickup if you post the neighborhood of your hotel.

Mahalo (Thank You) for all the reply's.We will be staying in the Fishermans Wharf area.Pakepf3