There are lots of potential issues with HL. Some were mentioned above. But they're engineering not concept. If you spend enough money they can be dealt with. But it won't be a short-stop Amtrak service to the Valley - to make it work well you would have to make the Valley flyover country just like the airlines do. Even just stopping in Fresno would increase the travel time substantially assuming comfortable accel/decel rates and the kind of speeds it seems capable of. So I think HSR and even enhanced Amtrak have significant uses. HL will be for the flyover traffic, and will certainly provide serious competition for the airlines.

Incidentally, the concept itself is nothing new. Look at SciFi as far back as the 1950s or even before - tubes through the Earth's core (!) like the pneumatic tubes used in stores at the time, but in a hard vacuum and free-fall with only a little power to get back into the station. Keeping it on the surface complicates things a bit dealing with terrain and existing populations/development, and makes the trip longer than a straight line would be - though tunneling through the SAFault near the Moho could be interesting.