Now, I am not trying to defend California's HSR, specifically. I agree with Musk that it appears to be very poorly done. However, the answer, to my mind, is to do it properly rather than propose a wild experiment with hand-wavy arguments as to why it would be politically easier to do. Do you really think the special interests that are making HSR so difficult and expensive would say, "Oh, do whatever you like with your tube."?
Now, in an attempt to end on a positive note, I do like his proposal as a possible next step beyond HSR. Rail can go up to 350km/h currently (perhaps more in the future--why wouldn't California design with this goal in mind?), but Musk's hyperloop is proposed up to ~1000km/hr. It is definitely an idea worth exploring, but I think it falls far short as a serious alternative to the current high speed rail plans.