I have no trouble imagining that the train can compete with flying between SF and LA. Even if the train has to stop in several backwater towns along the way.
The shuttle flights between SFO/SJC and LAX are completely unreliable. When I was doing the SF-LA haul regularly, I'd be delayed (delayed!) by 6+ hours at least once per month. That's longer than it takes to drive. Do you really think the high speed train will take that long to travel between LA and the Bay Area?
So what if the minimum time of the train is a little longer than a flight? The expected time enroute is still much less.