Kayak's own About Us page explains that position:
Unlike online travel agencies, Kayak is not a store. Online travel agencies are retailers that can only sell you the products on their shelves. Their displays are designed to sell the merchandise that make them the most money AND they tack on a service fee for each airline ticket booked which adds up for a family vacation.
Kayak is not limited to the size of a stockroom. In fact, since we don't sell anything, we don't even have a stockroom. Rather, we search for travel goods across the Web and provide details on hundreds of options. Since Kayak doesn't sell anything, there's no hidden agenda or biased displays.
Why anyone would buy a ticket through those Orbitz affiliate links is a mystery to us, as the fares from AA.com are clearly the cheapest. While the TechCrunch story says it was American's idea to pull its info, the comment that the airline sent to the Budget Travel blog blamed Kayak:
Kayak/Sidestep has advised American Airlines that they will no longer display our content.
We are disappointed and hopeful that this issue can be resolved in the near future so that American Airlines will again display on the Kayak/Sidestep sites.
The weirdest thing of all is that AA fares will remain on Farecast and Mobissimo--sites that also have Orbitz affiliate links.
· Trouble in Online Travel: American Airlines Ditches Kayak [TechCrunch]
· American Confirms that Kayak Will Stop Showing Fares [BT]
· American Airlines coverage [Jaunted]