The train cost more, but you enter the train in the city centre, sit down and relax, go to the restaurant car and eat a nice dinner, relax som more and you arrive in the destination city.
This works better in continental Europe, where you have shorter distances and high speed trains between the capitols, often making the train faster from city centre to city centre than air travel. Traveling from Chicago to SF by train is pleasant, but take a couple days, not a couple of hours.
I took the Amtrak a couple times from DC through WVA and have had several delays trying to get from VA to KY due to priority being given to the freight trains. I remember one trip having a one or two hour delay in the middle of no where while we were side tracked.
It is much, much more comfortable than a plane though.
Also IME Amtrak's prices are surprisingly reasonable. More like a place around the corner than like an airport food court.