To begin with, planes, as anyone who has travelled by air knows, are often late, and LAX-SFO is no exception. Continuing with Southwest for our example, they offer eleven daily flights between the two airports. With the exception of the early bird special, Flight 799 at 6am, they are often late, usually about ten to twenty minutes. That, of course, doesn't mean too much. Time spent at the airport waiting for the plane, however, does.
Southwest recommends arriving at SFO 60 minutes prior and LAX 90 minutes prior to the flight. Right away we see a problem. While the flight itself is only an hour and a half, the flight isn't the entire trip and we can already see that, of two people who arrive at the airport and train station at identical times, the train rider will arrive at his terminus first.
Of course, very few people travel for the sake of arriving at a particular airport or train station. Generally, the travel is a means to an end, located in the titular city. Here again we see an advantage to the train. Both the Transbay Transit Center and Los Angeles Union Station are in the heart of downtown, the hubs of their respective mass transit networks, and within easy walking distance of hotels and other destinations. By contrast, the airports are located twenty to thirty minutes away, not including the time taken to disembark the aircraft and wait for one's luggage.
What of the claim that air travel is cheaper than a train ticket? Well, it's true that if one happens to buy a ticket months in advance and flies on an off-peak day (Monday, Tuesday, and Saturday it would seem), a ticket can be had for only sixty dollars, including taxes and fees. Last minute travel as may often be the case for businessmen or travel on days that are more in demand results in higher rates of course, and we are not yet including parking costs.
Meanwhile, as of today, an Amtrak trip from Los Angeles to San Francisco can be had for only 56 dollars without advanced booking. It is by no means the most pleasant or fastest trip, involving a bus transfer to Bakersfield, the San Joaquin train to Emeryville, and then another bus to San Francisco itself. A direct connection that requires less employee hours per passenger and has more efficient travel will assuredly not rise above the price of an airline ticket. Furthermore, these comparisons are for travel today, when the true comparison is for travel ten years hence when the line has been built. As the price of oil continues to increase, the price of air travel, especially on shorter commutes such as Los Angeles to San Francisco which burn proportionately more per passenger-mile, will continue to rise. Meanwhile, California's electricity is mainly natural gas with increasingly larger amounts of renewables, such as solar. In fact, one of the reasons that Southwest is so cheap (and a major contributor to its profits) is that it locked in lower oil prices through hedging, but those hedges are about to expire.
So, will it be faster and cheaper to fly? Looks like that is just another myth.