Speaking from experience, there are many very "nice" hotels that allow guests to travel with their pets. For instance, both the Kimpton Hotel and Hotel Monaco are all very pet friendly, and never charge an extra fee, ever. Even certain of the Four Seasons hotels will allow you to bring your dog, if I recall correctly. I even once stayed with my dog at the Hotel Frontenac in Quebec City, which was quite lovely. There is normally an extra fee involved, and sometimes a pet deposit. But your statement that such hotels "are almost always the 'lower-end' offerings" is just absurd.
If you have spent any number of nights at any non-Disney hotels, I would bet money that you have stayed in a room previously occupied by a dog, and didn't even realize it.