Rental car tolls are a pain in the butt. I recently exited the Kansas Turnpike in a spot that doesn't have a toll booth. So I made a note of it, and went online after the trip and paid the toll - I think it was $8.
A couple weeks later, the rental car company sent me a letter saying they assumed I hadn't paid the poll, so they were charging me $35 "to cover their costs." I had to spend half an hour on the phone and email them my receipt, to "prove" to these effing thieves that I had paid the toll, and that there was no cost to them. They finally agreed to drop the charge.
So if you are going to use the toll roads at all, I would probably pay the $28 just to avoid crap like this.