I’m not familiar with Florida Toll Roads.
Do you pay the toll before you get on the road or before you exit?
Many businesses refuse to take bills larger than $20. If the toll is paid before you “use” the road, they have a right to refuse you service.
That being said, there’s more going on than just not wanting to take large bills.
I wouldn't say that the policy is right or wrong, but I know that I wouldn't trust a lot of strangers who wanted me to give them 99 dollars out of my pocket in exchange for a hundred dollar bill.