The recent controversies highlighting ESA abuse coupled with the DOT NPRM (which does not affect hotels) has put a spotlight on the issue. My guess is that hotels have come to understand that they need not waive pet fees other than for qualified service animals and the practice will spread.
If people want to travel with an animal which is not a service animal, that is fine. But, there is no reason why the fees ought to be waived and operating costs subsidized by one set of pet owners over another.