But that is different from stayed. Stayed in or at is all the same, motel or hotel.Perhaps this is the type of situation that's difficult to explain, such as why we say we are riding in a car, but on a bus; in a boat, but on a ship etc! At any rate, I think it's safe to say that whether it's in or at, depends on the context of the overall message. For example, there's a slight difference in meaning between:
a. We stopped at a motel ... (but there were no vacancies, so we didn't bother going inside).
b. We stopped in a motel ... (to spend the night).
Just my humble opinion,
This question wrongly assumes that the choice between in and at depends on the noun that follows. It does not. In and at mean different things.
Yes, you are thinking of the hotel as an institution that provides accommodation, not as a space defined by its physical perimeter. It is fine to say I'll be staying in the hotel if you mean within the confines of the building rather than in the annex over the road.At the same time, if you plan to visit someone and stay at a hotel, you'd say "I'll be staying at a hotel." To my ears, it sounds a little strange to say "I'll be staying in a hotel." What do you think?
In the context, is the hotel a building (in), or a business providing accommodation (at), or something else?