If a toll is charged on a road by the state and is then distributed elsewhere, it is effectively a tax.
But, there is the argument that the user fee is a tax. This argument is made in two ways.
First, as you have pointed out, a portion of the user fee is utilized beyond paying for that particular road. While this is true, the amounts are so small, and/or temporary, that they just don't calculate.
Second, the individual will, effectively, not have a choice. If he wants to get from point A to point B, he will have to use the road/pay the user fee. While this is true, there are other choices that can be made to avoid the user fee.
Those that use these arguments are are doing so on a absolute basis. Logically and reasonably, most people would examine it on a relative basis. That is, relative to the alternative of a tax.