Even without the check-in and security it is typically faster to fly (or drive) the places people typically go on a plane in the US.
The problem is that the railways are prioritized for freight traffic first, so the commuter train traffic takes a looooong time. My understanding is the freight movement by train is better in the US whereas the commuter train movement is better in Europe.
For example, I live in the Twin Cities of Minnesota. To travel to Chicago by different methods is:
By car: ~6 hours travel time
By train: ~9 hours travel time
By plane: ~1.5 hours flight time, call it 4 hours total travel time