I'd argue this happens because most hotels are franchises. Some owners will be more comfortable with pets in their hotels than other ones. There won't be consistency because "anti pet" owners can and will run franchises across multiple brands.

In terms of fees, there are three reasons why they might be expensive. First, they might be very high in order to discourage people from bringing Fido. Second, the hotel might see the fee as a way to make a profit. Finally, the fee might actually be used to ensure the room is fully cleaned for the next guest.

I used to work in a hotel with large pet fee. We fell into the third category above. Virtually all of the fee went to the outside company we hired to deep clean the room. The only way we made a profit was if we had two or more rooms that needed to be deep cleaned on the same day.