You make good points but you forgot to factor in the 2 hours early that you need to show up at the airport. Getting on and off a train can take only minutes.
I've only ridden Amtrak once but I guess there are also security requirements that do take some time also (as opposed to most European countries).
I've also experienced lots of unexpected delays on flights whereas trains seem to be exceptionally on time (especially in a country like Germany). You're also assuming a direct flight also (though this is probably more related to cost which is another issue).
All in all, a coast to coast journey that takes 12 hours vs. 7 doesn't seem so bad if:
- I can spend maybe 8 of it sleeping in a bed
- The difference is 5 hours
- I can eat some real meals in a dining car
- I can walk around reasonably