As they say, your mileage may vary. The air comparison really only makes sense in short corridors, and maybe some of the day trains if we're talking about places that don't have frequent/affordable air service (parts of the Vermonter, Adirondack, Pennsylvanian come to mind, though not necessarily the endpoints). I always recall a friend who, to get to Johnstown, PA from central NJ, flew from Philadelphia to Pittsburgh... I'm sure the travel time, with driving, security, and backtracking from PIT, came out about the same, but he insisted on making the flight.
When I'm on a LD train, I compare it to driving--without having to stop for meals, or to sleep, or to walk, or to use the bathroom, etc. Not all of the LD routes are time-competitive with driving, but once you factor in the stopping time, and any hint of traffic, they look pretty good.
But, even in the NEC, the competition varies. I've found, living in NYC and DC, that the real competition may be the new low-cost bus carriers (Megabus, BoltBus, etc.). Even though they can get stuck in traffic and, personally, I'm much more comfortable on the train, Amtrak can't really compete on price (and based on the sold-out trains I've been on, it doesn't necessarily have to).
Though I will throw out one pet peeve I've had lately: what happens when you get off at a station? Yes, sometimes you'll have someone meeting you, or you'll have public transportation, etc. There may be taxis, there may not. (I've noticed the latest timetables and website info don't list parking/taxis/etc. anymore.) In the best of circumstances, rental cars will be available near the station, but that's not that common. There are train trips I'd have taken that get NEAR my destination (let's say within a 2-3 hour drive at most) if it were easy to keep going... and no, taking a cab to the airport to rent a car isn't so "easy." It only adds fodder to those who would say, "Why didn't you just fly?"
