Switzerland tunneled through the alps for $12B. The issue isn't engineering.
After the Army Corps of Engineers built the Panama Canal in 1914, it was not all smooth sailing to build the Chittenden Locks in Seattle, between dropping the lake 10ft, reversing the course of/eliminating multiple rivers and streams and dealing with the fallout of that it was and still is quite an engineering marvel.
To build on top of a mountain range, there is a smaller overhead cost to survey, do an engineering/environmental study, cut earth, and lay down road but you literally have to pay that overhead for every few hundred feet because as the terrain changes, the equipment and other infrastructure you require also changes drastically. To build a highway you have to have strong ground to build on, which is why US freeways largely bob and weave all over the place instead of just going in a straight line, and civil engineers avoid weak ground where soil stabilization will be most expensive. On mountain roads, not only are the options for soil stabilization limited to very labor intensive methods, but you also often have no choice but to take a bad (expensive) route because you have to design safe turns and gradients. The problem isn't that the engineering is harder, there's just a lot more of it to do.
Also, United States property rights are pretty unique as far as Western countries go. To build a tunnel you'd have to get the mineral rights from every single property owner in your path whereas in most European countries, mineral rights are owned by the government. If you're going to compare a Swiss tunnel to any US road projects, you have to account for the massive differences in legal fees and land acquisition because whether you build above or below ground in the US, you have to deal with the property rights of private owners and all of the extra safety/environmental/etc regulations that come as a consequence.
I suspect some form of rent seeking (or likely multiple layers of rent seeking) is part of the problem.
Much of the relevant land in the mountainous parts of the Western US is owned by the federal government so I'm talking mostly about the actual construction costs. Unfortunately, the high speed rail is useless without tracks to and from the mountain sections so the cost of obtaining right of way still matters. From my understanding, the Swiss tunnel is an extension of an existing network, so the 36 miles of tunnel didn't depend on lots of new above ground construction and the risk that comes with it.
For example, the interstate 70 expansion through the Rocky mountains that connected the western and eastern halves of Colorado cost $800 million per mile for 12 miles, even though all of the land was already owned by state and federal governments. There was little opposition, it was badly needed, and the project went very well (winning several awards) but it still cost over 40 times more than initially predicted because it turned out that building a massive highway through the Rockies was a lot harder than anyone had thought.
People only shut their mouths when they get threatened into a fearful silence, and/or sometimes if they get bribed enough.
Otherwise, you'll always have a substantially sized group of complainers dragging down a project this big, and the complainers leech into operations and mysterious expensive mistakes erode the budget of an already expensive operation.
There's just enough shrug factor here for people to not care about how much gas they burn driving to places that might not be very exciting to begin with.
Many would just as soon not have to travel at all, and even more would prefer to not be taxed so as to pay for trips they personally don't want to take to begin with. Most people just want their actual lives to be generally easier.
Without confrontational intimidation, bribery is probably the only other political lever to press in the United States.