I don't know what the official policies are, but I can see a hotel giving you credit for hotels.com. It is fundamentally different from priceline and hotwire in that you know what hotel you are choosing.
I think one of the primary purposes of a hotel loyalty program is to get you to choose that hotel chain when you stay. On priceline and hotwire, you are not choosing a specific hotel chain, but just going after a cheap rate.
Hilton's web site, for one, specifically mentions this:
"Eligible Rate stays are stays at all rates except ... stays booked via Priceline.com, Hotwire.com or similar booking channels where the hotel brand is unknown at time of purchase."