As others mentioned, you'll miss some really nice miles if you skip the San Francisco area. Do like the other above mention and take the coast road south through Marin County, cross the Golden Gate bridge (VERY cool on a bicycle!) and then follow the Pacific coastline (generally) to go farther south through the Presidio and the west edge of Golden Gate Park. Don't plan on hitting SF until about 9AM and you should only experience light traffic in the City. And don't go through the center of town; I was there last January on a business trip and it was amazing how many homeless/crazy homeless are in the streets up there! Heck, I'd be more worried about the crazy traffic on Hwy 1 south of Big Sur than the traffic along the coast between SF and PAcifica.
Q: If you don't like San Francisco, what are you going to do when you get to the Los Angeles area? Skip the whole thing and just take Amtrak to San Diego?