The question to ask is "who owns the rail lines?". That matters for having a good rail system. It's basically the same problem for why the US doesn't have fiber internet available everywhere, too.
I think what it comes down to is that if automobile companies had to build and maintain the roads, we certainly wouldn't have so many cars. But railway companies need to build the train lines, while competing with taxpayer funded automobile infrastructure. It's not impossible (see Japan) but also not easy.
The interstate automobile road system got built through judicious use of eminent domain. That avoided all of these issues. Amtrak doesn't have the ability to do that.