You are right, but when an airline stops flying to a certain airport, it usually means that the airport itself does not have sufficient traffic to justify airlines flying to it anymore. Airlines choosing not to fly to MHT and therefore flyers choosing not to fly from there is a result of the airport itself becoming less popular, not vice versa. The effective way to fix this issue would be to provide an easy and fairly fast way of getting to the airport (i.e. Commuter Rail), and with the "Regional Rail schedules" currently in place, this just makes it even more convenient for flyers to get to MHT in just over an hour. And if the shuttle buses serving the airport are frequent and don't take too long to get to the terminal (they just have to cross the access bridge, so that won't be a problem) then that wouldn't be much of a problem either.
The only way this can be messed up in a way is if the MBTA only has half the amount of trains actually going as far north as Manchester, this would be a similar case to the situation with T.F. Green Airport, which has just about half as many trains as Providence does, which not only caused it and Wickford Junction to have much lower ridership than originally foretasted, but also caused the T.F. Green Airport to not benefit as much from the Rail extension as it could have, though luckily for them, T.F. Green seems to have enough of a population around it to still provide enough people choosing to fly out of them rather than out of Boston if possible, a luxury that MHT does not have. This is part of the reason why I believe that when this extension does happen, all Lowell trains should be extended to Manchester, as otherwise, Bedford/MHT and Manchester stations would be underutilized, I also believe that Wickford Junction should be double tracked and all Providence trains extended to terminate there, but that is a discussion for a different thread.
Photo by Alan Thomas: NYNH&H I-4 Pacific #1372 proudly thunders through Forest Hills as it makes its way to Providence R.I.