As someone who boycotted the TSA for like 5 years and only took Amtrak, the tickets are not always cheaper. I mean sure, you can get across the country for like $100.
Even when I was doing Boston-Baltimore on the Acela, it was routinely slightly cheaper to fly.
AmTrak is designed to suck. Freight lines own most of the rails, and while they are required to give priority to passenger trains, they avoid this in several ways. Like having the freight trains too long to fit on side rails so the passenger trains are required to stop instead to make way.