All of this comparing airline service to train service for long-distance trips is ridiculous. Clearly, unless you have some medical reason why you can't fly, then the only practical way to travel a long distance is by flying. The distance cutoff might be 4-500 miles or so, and that depends whether there's direct air service between the places you want to travel, the time it takes to get to the airport, clear the formalities, etc. Thus, even the shortest flying trip will take at least 4 hours or so, even if the flight itself is only 30 minutes.
A long-distance Amtrak trip is at least overnight, and is a completely different product, similar to flying only in that they promise to deliver you from point A to point B.
As far as comfort and value, the longest you're going to stay on a plane for a direct flight within the 48 conterminous United States is about 6 hours. That's a little less than the journey time of an Acela from Baltimore to Boston. There's no need for lie-flat seats and other such frills for such a short flight. Most people do quite well in coach. As far as ticket prices, I've heard all these ridiculously low fares for both coach and first class, but every time I try to book a trip, the fares are a lot higher, and the ones that are reasonable usually are nonrefundable and also by the time you re-bundle the extra services that should be included with all airline tickets (like checked baggage), the final price isn't so cheap. Thus, at the very least, if one insists on comparing train prices with plane prices, one should use airfares that have similar services to the basics that you get on Amtrak -- checked baggage, flexibility, and refundability. (Yes, I know Amtrak charges some cancellation fees, and you can only get a full refund to a voucher, but a lot of those cheap airfares are totally nonrefundable, so if you need to cancel, you just have to eat what you've paid.)