Well the airlines also have another large advantage. They are originating from hubs and terminating at hubs and have traffic coming in from all over the map. Whereas amtraks hubs are microscopic compared to what the airlines have.
You have Washington with service south to Florida (won't really pull air shuttle passengers), service to Virginia points, and the Capitol Limited again not really pulling passengers from the shuttle.
Next down the line you have Philly which has the keystone trains into Harrisburg and the Pennsylvanian. Not super likely to pull a lot of passengers from shuttles. But likely better than DC.
Next up we have New York which has the empire corridor, and the Lake Shore to upstate points. Likely this does draw some traffic and provide decent connecting traffic.
The last hub you have is Boston and that's just he poorly timed for hub and spoke Lake Shore. And the Downeaster aside from the main trunk.
While LGA, JFK, EWR, BOS, PHL, BWI, IAD, DCA all have connecting service from the world wide. You can fill those planes even if Amtrak took all of the Shuttle passengers just off of connecting passengers.