The situation with flying is a bit more nuanced than you make it out to be. I fly to NYC and DC from Boston pretty regularly for business. With TSA precheck and dedicated security lines for the regional shuttles, it usually takes me 2.5 hours total to make the trip. Of course, that requires driving to the airport and taking a cab once you land at your destination.

These legs are serious business for the airlines that run them, as compared to Amtrak who isn't going to be able to do anything for you if you get stopped due to freight. For example, the flights to these destinations run once an hour. If you show up at the airport before your flight and there is a seat available an earlier flight, the ticketing machine will automatically prompt you to re-book for free. That flexibility is not something you're going to get on a train.

All of that said, for personal travel I usually take Amtrak. Most people can't risk the multi-hour delays that can result from train travel when they are on the clock. But when I'm on vacation, it doesn't matter to me either way and the train is a much more relaxing experience.