You're required to keep the dog in the bag under the seat for the entire flight so they shouldn't really affect cleaning.

I have two issues with the fee.

1) It only covers one way. For a round trip itinerary you are looking at $250 - $400 for the pet fee. That can be more expensive than the actual ticket.

2) Your pet counts as your carry on item. I would be a little less bothered if the dog was allowed in addition to your carry on and personal items or if the airline included a free checked bag with the fee to offset the carry on. Since the dog counts as your carry on, you have to pay an additional $25+ each way to check a bag you might've otherwise carried on the plane.

That's $125 and you have to keep the dog locked up in a bag the entire flight, so I don't see how it could affect their cleaning.

On the other hand, it does mean that effective ticket prices would now be more expensive for people who have service animals. While not necessarily malicious, it is a form of discrimination. Airlines don't charge overweight passengers extra for seatbelt extenders.