This is also true for car rentals and hotels.

My theory is that the marketing plans go something like this: those going to AA.com, hertz.com, hilton.com, etc. are assumed to be sensitive primarily to brand recognition and brand loyalty, not quite so much to price. OTOH, those going to Orbitz, etc., are very price-sensitive, and less interested in a particular brand. So the price structures marketed to these different customer populations are different.