I've done it a handful of times, because the deal was better than if I booked on my own.

BUT

I have always emailed both the hotel itself and the airline (in the case of booking a package) to confirm that I am booked for what I think i am booking. I've done this with Rondel, Footeprints and Seastar and fortunately all was as I booked. But it does pay to double check directly with the hotel when booking through Expedia, Travelocity, Orbitz or whatever.

You can email ahead of booking too, to find out what "ROH" or whatever room category you book generally means at their property.