I had the identical thing happen to me on the Dallas Tollway, but why, I don't know. I was told by rentalticket.com that they had a photo of the license plate of the Hertz car that I was driving when I "ran through the tollbooth without paying." They also said that it was taken at 11 PM. I told them that I had picked the car up from DFW at 4:30 and was sound asleep in my hotel room in Denton at 11 PM, never having been in Dallas. I had to fax them the copy of my Hertz agreement, my plane ticket, and my hotel receipt. They still refused to dismiss it totally and said that they would have to charge me an "administrative fee" of $2.50. It wasn't worth further argument for $2.50, so I let it go at that point. What a ripoff.
By the way, I am President's Circle and it didn't save me from this travesty. If this happens again, I'm taking my 50+ rentals a year back to AVIS.