$56M doesn't really apply here, even if we were talking about a transcontinental hyper loop. I don't know if you've ever driven across the country, but there is a whole lot of empty space. Building stuff there is significantly cheaper than where stuff already exists.
A 4 lane highway in rural areas costs about $5 million per mile (*). And while a road is not an enclosed vacuum tube, the vacuum tube would be many more times complex to build (and maintain) than the road - for example, there its the infrastructure needed to keep the hyperloop pumped down to its working pressure, as you can be sure that leaks will occur.
But that infrastructure will have to be dispersed across the length of the hyper loop, as a pumping station in LA or NYC will not be able to deal with a leak in the midwest until the air introduced in that leak makes its way to either end of the loop - meaning both a huge volume of air, and a huge lag time until it gets there. And huge vacuum pumps will not be cheap, and will have to be powered by something. So there you are building not only the hyper loop, but at a minimum HV transmission lines for the pumping stations and possibly power stations as well (be they solar, wind, nuke or coal), as well as the roads needed to reach that infrastructure . Plus as you say .. you are doing it in the middle of nowhere,which is going to jack up prices in its own way.
So it does't take much for the cost per mile to start adding up.
* $5 million per mile cost for a 4 lane highway is taken from the American Road & Transportation Builders Association website. And it rises to $9 million in urban areas.