Airports are in-effect giant malls. They rent out space to shops, and airlines. Ostensibly the airport authority has set the pricing to maximize net income. For example DIA's authority is the city and county of Denver. JFK's is the Port Authority, which includes EWR and LGA, but also much of other transit in the area including LIRR, and MTA, but includes seaports, bridges and tunnels, and ... real estate.

ATC is run by the FAA whose budget is set by Congress. Everything is paid for. There are no per use fees. Landing fees are not federal, they're imposed by (local) airport authorities. The weather, flight service, ATC, national airspace system, navaids, all of that stuff is provided by the federal government.

ATC and FAA don't want to be in the business of collecting fees. And airport authorities don't want them to because it would necessarily cut into their take, and it would also mean they lack exclusive control to set pricing and thus demand and thus limit their ability to maximize income. It's a shopping mall.