I have spent two awful flights having allergic reactions to dogs in the vicinity...I would prefer a hamster in my aisle over a dog!
I am not sure how they can discriminate between animal type as long as they are are of a reasonable size and contained in a appropriate pet carrier...but, I for one, would like all pet owners to be in on section of the plane with separate ventilation...it really isn't fair that other passengers should suffer.
There is no section of a plane with different ventilation, unless you want to stick owners and their pets in cargo. There is a lot of expense to bring an animal on board. You have to pay for the animal to be allowed on the plane and for the vet certificate.