RVLimey, I had the same feeling, even though people were saying that it's "doable" to drive through the city. I drove the way you are proposing, in reverse, a couple years ago, and it was fine.
Coming south, go past Santa Rosa to Novato and get on Hwy 37. Or you can get off at Petaluma on Lakeville Hwy and take it around to Hwy 37 (which is what I did). Hwy 37 to I-80 south to 780 to 680 south, cross the bridge and you're home free. Yes you can then take 680 to 580 over to I-5 or 99. What I did (in reverse) was take 680 all the way down to San Jose and get on 101 again.