I read in Aviation Week that the airlines pay something like 95% (or thereabouts; I don't have it in front of me) of the monies collected in fuel taxes, and that this new plan would bring their contribution down to 72% (again, or something), which is more in line with their usage.
It occurred to me that the airlines need a sophisticated ATC system more than the GA and business planes do. That's not to say the smaller operators don't need it; certainly, they do. But they have more options as to when, where, how, and if they fly. They have a smaller and more understanding clientele. They don't have to convince the little old lady from Ipanema that they are as safe as Amtrak or Greyhound. Their need for full ATC services is somewhat less than that of the airlines.
If ATC were a private business-- were it my private business-- I'd find an excuse to charge the airlines a little more. Maybe around 20% more. Why? Because you make your money where you can. The airlines themselves understand this; it is why First Class is priced THREE TIMES as much as Economy Class.
So, I'm unswayed by the argument that FAA user fees are more "fair". A product or service is worth what you can get people to pay for it, not what it costs you to provide. What it costs you to provide is completely irrelevant. If we want a robust, healthy system, we will continue to fund it in a way that factors in people's need for it. Fuel taxes are simple, practical way of approximating that.