Los Angeles to San Francisco is the busiest air corridor in the United States with an estimated 60 million passengers per year expected by 2020. It is one of the top 20 corridors in the world.
The airports can't handle much more traffic and it costs a substantial amount of money to build new ones (upwards of $20 billion), connect highways, etc.
So high speed rail makes real sense. There isn't even a place to put another airport in the bay area unless you stick it way out of the way.
The links to San Diego and Sacramento don't cost anywhere near the price of the main segment of LA to SF and are just there to complete the system. I don't even think they are part of the first stage and may never end up being built.