That program is around $3.35BB of the $10BB total FAA expense.
Essential Air Service subsidies Airlines serving rural communities which significantly increases overall ridership. Air Transportation Safety and Stabilization Act as just one example was 10 billion in loan subsidies after 9/11. Another example most Airports are heavily subsidies at least during construction, but so is some airline infrastructure like Indianapolis handing over $300 million for a United Repair shop. The military intentionally creates a huge stream of trained pilots without costing the Airlines a dime.
All of this is intentional so no one subsidy seem all that large, and adding up a thousand little pieces take enough effort that nobody complains.
PS: "Per passenger EAS subsidy in the 48 contiguous states plus Puerto Rico ranged from $10 to more than $977 per passenger in 2014" but it's only ~300 million per year so no big deal right. https://en.wikipedia.org/wiki/Essential_Air_Service
My plane ticket receipt contains fees for half a dozen various government costs, including airport fees and a general US transportation tax. The FAA is pretty trivial, having a budget of just under $10B out of total American spending on domestic air travel of more than $800B.
https://www.transportation.gov/sites/dot.gov/files/docs/miss...
https://www.statista.com/statistics/207075/domestic-travel-s...
For all I know air travel may very well be subsidized, but you'll need to point to some serious numbers for it to be anything like the money that Amtrak hemorrhages as a fraction of its revenue.