I live and ride my bike in San Francisco. First off, there aren’t a million people in San Francisco, let alone a million cars! Second, there are many bike routes throughout the city. Third, going from north of San Francisco to the south of San Francisco will involve buses from, at least, 3 different counties. Finally, San Francisco is a nice city to ride a bike through, if you know the best way.
I’ve mapped the route I take from the GG Bridge to Ocean Beach, where you pick up the ACA route. You can see it here:
GG Bridge Alternative at Bikely.com .
If you’ve never been on the GG Bridge, there is a huge difference between riding a bicycle over it and going across on a bus. Do what you want, but I think it would be a shame to ride down the Pacific Coast and skip San Francisco.