There is adequate rail transport from SFO to downtown San Francisco where you can rent cars. Why pay the extra airport fees even at Santa Rosa?
You could also fly to Sacramento, Oakland or San Jose.

If you're doing this to save car rental fees at SFO, do as tf says (take BART to downtown SF and rent the car there). If you're doing this because it's "confusing" to drive through San Francisco - well, it's not, so rethink your plan.

The trip from SFO is not confusing at all. It is very well sign posted. If one were to get lost between SFO and the GG bridge -- I'd honestly worry about their ability to drive the rest of their itinerary.

So if it is primarily for simplifying the journey - I wouldn't bother taking the airporter. If you can get substantially better rates at Santa Rosa - that might make a difference. But it would have to be a significant savings to make up for the cost of the airporter.

Going into SF on BART to save a bit on a rental would make sense if the rates were enough cheaper to make the time/hassle worthwhile.

I assume you already booked your flights - so suggestions about flying in to other airports is probably pointless. (But if you haven't yet booked, let us know and we can explain the pros/cons of other airports)

No we have not booked our flights yet as it is for January so just getting some ideas as to what would be easier. We have driven from the airport and once from downtown and did not like dealing with the city traffic. What we saved on picking up rental car in the city we spent it on a hotel for a nite so wanted to try different this time. Flying into other airports could be an option but would be further away from where we want to go would it not?

As a long time SF resident, I don't like to drive in SF itself - usually take public transport wherever. It looks like there's not really any cost savings in Santa Rosa rent a cars if you take the airporter but it may be less hassle - it's only $60 round trip and saves a lot of driving that isn't very pleasant. Same prices from SFO-Santa Rosa as OAK- Santa Rosa so if there's any cost saving to fly to OAK that's an option too.

"it's only $60 round trip "

But that is $120 if there are two of you.

Driving in SF in general is not fun. BUT the drive from SFO to the GG bridge is very straightforward IMO.

The problem w/ flying into any N. Calif airport in January is weather. SMF can be fogged in for long stretches.

If the drive on 101 freaks you out then fly into Oakland. Freeway most of the way to Napa.

My point for the Airporter - if you really don't like driving, as I don't here in SF, you're not missing much not driving from the airport and I'd certainly consider spending the $$ to avoid a long-ish boring drive. Having been on several road trips recently (SF to Northern Sonora Co, SF to Mendocino area) as well as trips to Marin,) traffic is awful, the drivers w/ the speed limit now 65 routinely drive over 75, and it's just not pleasant.

Especially if the OP is coming in Jan when there may be rain, I'd definitely consider the airporter to Santa Rosa.

Just another point of view form a long time resident

If you can fly Alaska airlines to Sonoma County airport, you can avoid the whole ugly mess of San Francisco since you don't want to see any more of the city. http://www.sonomacountyairport.org/alaska-airlines-sts
I like the logo of the airport with Snoopy sitting on the wing of a biplane. (Charles Schultz airport).
The schedule is posted on my link for Alaska Airline