It can't possibly take significantly more time to take a train from Macon to Atlanta than it does to get through security at the airport, get the flight boarded and off the ground, and then get to Atlanta. In fact, it almost certainly is more time-efficient as well as less expensive to take the $110 RT shuttle from Macon to Atlanta airport noted in post 301 of this thread.
I was actually referring to Brainerd - Minneapolis. Macon - Atlanta is a bit harder to compare apples-to-apples, since the airport near Macon flies to BWI twice a day instead of ATL (the flight appears to be $89-$99 each way.) However, there is an airport shuttle between Macon - Atlanta at $41 each way, running 18x/day, plus flights on Spirit for around $50 one way to BWI (with multiple other options on different airlines for a bit more.)
They both serve a role. Not everyone has the luxury of time that Amtrak requires.
And not everyone has the money that EAS service generally requires. Why should the US Government be spending money to subsidize travel in a way that's still expensive for a lot of people if a cheaper alternative (both for the US Government and for the passenger) either exists or could exist? Those who value time above all else could still buy air service off of the open market, while the government should support a baseline level of connectivity that's affordable to as many Americans as possible.
As but another Minnesota example, let's look at International Falls. There's currently subsidized air travel to MSP via the EAS, with a $3,388,905 annual subsidy from the federal government. The direct ticket runs $295 RT, though that segment's cost is likely reduced somewhat if you're booking it as part of a connecting itinerary with Delta (so instead of being a $295 upcharge, it might only be $200ish more than a RT ticket direct from MSP to your final destination.) Right now there's a once-monthly bus service to Duluth, a city with an airport that doesn't require EAS subsidy, through the local transit agency for $25 RT. If that transit agency was given that $3.3m annual subsidy instead of Delta/Skywest, could they offer that service daily (or even multiple-times-a-day service) at that $25 RT price, adding a stop at the Duluth airport? If so, that'd be a win in a few different ways - residents would have an affordable daily connection to both the intercity air network and the intercity bus network, along with a daily connection to a larger city for shopping and medical appointments, the city would have a much cheaper way for people to come into town and visit, other airlines could compete for that business more easily out of DLH instead of starting at a major disadvantage, etc.