Absolutely and if they have their own website, you usually get a better description of the hotel and facilities. In addition I usually check out the reviews on www.tripadviser.com I know they have come in for some criticism recently, but I've never had any problems with their reviews
edit: some hotelliers I've spoken to say that the hotal search sites take a 10% referral fee, and by dealing direct with the hotel you will usually get at least 10% off, plus you don't normally have to pay until you arrive or even on checkout. Some of the referral sites take the money upfront