That's not to say the government couldn't fund it as a transportation infrastructure project, but that's not the Silicon Valley model, and the funding is much smaller and harder to come by than defense spending.
The problem isn't really just to spend "more" on R&D -- have you seen the defense budget? Hyperloop would be a blip. The problem is deeper.. it's that our system is not set up to funnel taxpayer funds into public services like this. IMHO for political reasons. Running it through the pretext of defense makes it harder for citizens to question how funds should be spent and who they should benefit.
We need political change to make sustainable public transport projects like this take priority. Just like we need it for education, social welfare, etc. It's easier to control people when you tell them the Russians/terrorists are coming so we have to take your money and fund defense.
And if that's the case, that also suggests an answer to all of this. Spend more on basic R&D.