Geographically, it does not make sense for Amtrak to run into San Francisco, based on their current service around Northern California. The south end of the Capitol Corridor is San Jose, and Oakland is the current terminus for the California Zephyr and is the Western end of the San Joaquin line through the Central Valley from Bakersfield. The maintenance facility at Oakland caters to the Amtrak California fleet and serves as the turnaround point for the California Zephyr. It's been this way since the original Western Pacific trains terminated at the same place the California Zephyr does today.
A general rule for rail travel in San Francisco: If you arrive in Oakland by rail, it's easy to transfer to BART at Oakland to get across the bay. If you're coming from the south, the Cal Train service on the former Southern Pacific Peninsula Corridor is excellent. This line has undergone extensive rehabilitation in the last decade, and both express and stopping services are offered. There is a station that serves the SFO airport with both BART and Caltrain. The commuter services, coupled with BART rapid transit and the MUNI streetcar system make San Francisco a very interesting place to travel by rail.
There are plans to electrify the Peninsula Corridor and run high speed trains into SFO.
It will be interesting to see how it all evolves.
http://en.wikipedia.org/wiki/Caltrain
http://en.wikipedia.org/wiki/Capitol_Corridor
http://en.wikipedia.org/wiki/San_Joaquin_%28Amtrak%29