Part of moving in to a new place is finding the various vendors.
Petaluma Market at the intersection of Western Ave and Keller Street (the extension of 5th). Decent basic grocery store.
G & G Super Market out near the college is huge and has a decent produce section.
I still miss United over in San Anselmo.
Taylor at Fruit In Hand is knowledgeable and will do everything from preparing your beds and soil to managing your garden.
Hardware & Lumber
Used lumber is available at the dump, go towards the commercial area, bear right which will actually be a path that crosses back left after the scales, and drive to the top of the hill.
New lumber calls for a trip north: Mount Storm is the place to buy hardwood lumber and cabinet and drawer hardware. Higgins Hardwoods in Rohnert Park is a favorite of flooring and cabinetry guys, but has a minimum $250 order size for us lowly individuals. Mead Clark in southern Santa Rosa is your basic lumber yard, a step above Lowes or Home Despot.
Tomasini Rex Hardware at 4th and B has great service, but I've also had some interesting and useful help, against all expectations, up at Orchard Supply Hardware. I've also found some diamonds in the aisles at M Maselli and Sons, it's like someone stocks the high end good tools almost by mistake, so I'll sometimes check there before going further afield when I'm looking for good tools.
Sonoma County Airport Express runs from SFO (hourly) and OAK (every other hour) to the Petaluma Fairgrounds.
You could also take BART to San Francisco and get on the Golden Gate Transit bus headed up here, go to http://goldengatetransit.org/schedules/pages/Bus-Schedules.php and click on the appropriate sub-heading under "ROUTE 70/71/80/101", that takes you to the Copeland Street Transit Mall.
Also investigate BART to the Golden Gate Transit bus in Richmond (route 40, I think) to San Rafael, transfer to the 70/80/101 up here. I'm guessing the city will be easier.
On the way in, if you do take the BART into the city and then transfer to the bus, note that many higher end hotels will happily check your bags for a small fee. So you could BART to SF, hang out in the city without your bags, and then take the bus up later.
What we usually do when we go into the city is drive down to the Larkspur Ferry Terminal and take the ferry in. You get to see the bay, Angel Island, Alcatraz, the Golden Gate Bridge, and don't have to drive or park in the city. It lets you off right at the end of Market Street.