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) I

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.