The fuel tax is proportional to how much fuel you purchase, not your use of ATC resources. Consider a flight school aircraft performing multiple practice instrument approaches while receiving ATC services versus a crop duster not receiving any ATC services. The flight school airplane burns a lot less fuel than the crop duster and pays less even though they use more services.
The infrastructure to charge for ATC services, landing fees, etc is already in place. Airports such as BKL will send a bill for the landing fee to the address on the aircrafts registration. The FAA charges for ATC services if you don't either land or takeoff from a U.S. airport. Billing for services isn't difficult.
The quest for precision in allocation of ATC costs is not worth the cost in the form of the safety disincentive, IMO. I would also argue that having an effective air traffic control system is a benefit to everyone, not just to the people who happen to be using it on any given day.