Riding over the Carquinez Bridge into Vallejo and then through American Canyon to get to Napa is, in my experience, is a pretty decent way to get from the East Bay to Napa. Hwy 29 through American Canyon can be almost entirely avoided except for a three mile stretch that generally has a wide shoulder.
Unfortunately, the safest way to get from Napa to Petaluma is probably also the most challenging. It entails about 3k’ of climbing over Trinity Rd and Sonoma Mtn. Rd. after which you reach Petaluma Hill Rd and are relatively close to Petaluma if that’s your destination.
The Vallejo-American Canyon segment is from mile 17.6 to 27.5, after which you’re almost entirely on side roads, bike lanes and bike paths into Napa. Note that after the Trinity Rd climb you can descend more directly into Glen Ellen by staying on Trinity instead of descending on Cavedale.
The route I linked above is almost exactly 200km. I can submit it as a perm if anyone is interested in riding it. It ends at Comova Cycling, a guiding business I operate with onsite accommodations.
—Steve