Going back on topic, I just remembered that I did stay at several non-chain hotels in the US last year; one of them was the Yellowstone Park Hotel in West Yellowstone. It was surprisingly pretty decent considering the last minute nature of the trip; I was expecting to stay at least a couple of hours outside the park due to lack of availability.

Anyway, I think it really comes down to researching beforehand. In the past going with a major chain was easier as consistency was better guaranteed and it was harder to get information on smaller places, but now that there's TripAdvisor, FT, etc., it's easier to be satisfied with a non-chain hotel.