A leap of faith
First, you cite that air travel could take longer than high speed rail. But you neglected travel time to a high speed rail station (there are only a few stops, even in high density areas such as LA it could take an hour or more during rush time there to get to a high speed terminal) and possible security checkpoints (a high speed train is just as vulnerable to terrorism as an airplane).
Second, the original cost of the rail was supposed to be only $45 billion when the original ballot issue was passed in 2008. It's grown to $68 billion now -- about $16,000 a foot -- before a single rail has been put down. We have no idea what the final cost will be, but no doubt it will be much more. Think of Boston's Big Dig, or metro Denver's FasTracks. In any event, the project will depend on heavy federal subsidies; the recent California vote to press forward was to meet a federal deadline for $3.2 billion in federal funds. That's only the beginning.
Third, I don't know why California has to be energy neutral any more than any place else has to be. That's the whole point of trade. I doubt you would argue that California should be revenue neutral in building the thing and forgo federal funds. But let's play that game. California has huge oil reserves offshore that it has never tapped. With new horizontal drilling techniques which you decry some of them can even be tapped from onshore. Hermosa Beach is currently debating about whether to allow such a project. The liberal residents there are having a hard time deciding between their distaste for oil and the need for adding revenue to the city coffers.
