Not if you are a regular traveler. In that case you have global entry and/or clear, and aren't checking a bag. Depending on the exact terminal you can get to the airport about 15 minutes before boarding, 45 minutes before listed departure. The bulk of the advantage is the location of the terminal stations, which is real but not as significant as it is being made out here. I mean maybe if you live right at Penn Station and your meeting is right by Union Station, but if you coming from, say, LIC and going to Georgetown, you may be happier with LGA and DCA than NYP and Union Station.
You're absolutely correct about the comfort points, but price should be just as strongly in the train's favor and it isn't.
The regular travelers have voted in numbers for Amtrak between DC and NYC over air travel, preferring it for the last decade[0]. They have been growing the number of trips and have even been able to go further up market with the new Acela nonstop this year. The truth is, passengers are voting with their dollars for the train between NYC and DC.
NYC and DC don't really project to other metros. Travel to and from Penn Station vs the airports is a non-trivial consideration to passengers. It is expensive or time consuming or a PITA to travel to JFK/LGA/EWR on public transit with a bag. I lived in Brooklyn and made the NYC/DC commute 15 or so times a year for many years and that was a significant issue for me, it just wasn't cost or time effective to fly in _NYC_.
I now live in Maine and wouldn't consider for a second taking the train to NYC. I'll fly out of PWM or, if I want flexibility, drive there. There is a non-stop bus that I'd prefer, too.
It helps that due to a mix of incompetence and lack of support from the governor‘s office that there is no direct train link through Boston that a train from Maine might use to get to NYC.
Georgetown to Union station is about four miles and the circulator bus will take you there for a buck. DCA is about six miles and accessible by Metro. Seems about the same.
You're absolutely correct about the comfort points, but price should be just as strongly in the train's favor and it isn't.