Problem #1 ...
A fuel tax is not a true user fee, but it's a reasonable surrogate for one. It's allocated to the user in a way that is roughly proportional to a motorist's use of roads overall but not to any one road at any one time (an important distinction that will be seen in #2 below). A toll is a true user fee that is allocated to the user in a way that much more accurately reflects the motorist's use of specific roads at specific times. Tolls had historically lost a lot of their appeal because the cost of collecting them diminishes the actual revenue being raised, but they are starting to get more attention now because the technology for electronic tolling at highway speeds has matured.
Problem #2 ...
The problem with a "gas tax as a surrogate user fee" approach is that the taxes are paid without any regard for the actual use of specific roads at specific times. In other words, the tax is paid up front and then the motorist drives when or where he pleases afterward. This may not have been a big deal when the U.S. was constructing highways all over the place, but the obvious flaw can be seen in the growing traffic congestion on our roads. Our system of fuel taxes is comparable to a supermarket that doesn't charge for individual items, but charges each customer a flat monthly fee on the first day of the month and then allows all the customers to take whatever they want from the shelves for the rest of the month.
Because this arrangement eliminates the direct allocation of costs for each item in the supermarket, the business model is doomed to fail for two reasons: (A) the customer has already paid up front, he has a huge incentive to empty the store every time he walks in the door even if he doesn't need 99% of what he buys; and (B) since the supermarket has already collected the money up front, it has no incentive to provide any kind of quality in the products or the shopping experience. And the supermarket has to keep raising the monthly fee to cover for the excessive drain on its inventory. The end result is a dirty, overcrowded, overpriced supermarket filled with crappy products on the shelves. That's sounds an awful lot like our nation's highway system, doesn't it?
The supermarket analogy is not a good one.
The toll theory sounds fine but it lost favor because it is not practical in a universal sense - a means applied to travel on all roads at all times. I don’t even think there is now in all cases rock solid restriction of toll revenues to the maintenance of just the road the toll is collected on.
The theory applied universally would mean you’d start paying a toll, or series of tolls (collected by different collecting agents/agencies) as soon as you left your own property. But we do not even apply user fees universally - for all roads. Within states and outside of the Interstate and State designated highways. roads, whether local or county designated roads, are paid by a mixture of state fuel taxes, state, county and local general revenues.
So, if there is an argument for toll roads over fuel taxes, it could only be applied at this time to roads that are Interstate highways, U.S. highways, and major state highways for which fuel taxes, federal and state, supply the bulk of the revenue. I also do not think THAT would be seen as practical to all cases it would have to be applied to, and any benefit would be offset by the costs of running any toll collection systems.
THE real biggest problem is the combination of (a) not all fuel tax revenue is restricted to supporting roads and nothing else, (b) politics and corruption in the setting of road priorities in the states, (c) waste and corruption in the performance of the contracts for road building and maintenance. Arguments about the fuel tax are a diversion from the real problems, all of which would continue to plague the use of the revenue no matter how it was obtained.