This seems like a very similar (and big) problem to Europe. Trains are just so expensive. UK it is unreal, I'm pretty sure some days you can fly from London to edinburgh for 1/10th, on a bad day 1/5th of the cost of trains. It just doesn't seem worth it. Clearly something about the economics of trains just doesn't work, especially when compared to mid-distance trips where cheap airlines also exist.
I came here expecting to see that the "free market zero regulation" of the US, and business sense would mean quite a cheap fare for this train, but no, it's just as bad as europe.
Even though they are supposedly the ultimate green mass public transportation, trains really need to get cheaper to be a serious alternative for cars and cheap airlines, as you also point out.