This is a bit of a hassle but probably not a huge deal. Yesterday the folks at Budget Travel reported that American had decided that it would no longer allow the popular airfare meta-search site Kayak to list its fares. It seems there was an apparent tiff over the fact that Kayak linked customers looking to buy over to Orbitz instead of the American site, which presumably means that American then had to pay fees both to Kayak and Orbitz.
I, like many, find the metasearch sites invaluable so I'm hoping other airlines won't follow suit. But it's a pretty safe bet they won't simply because the airlines know that we like them and use them and if they start pulling themselves off the sites they'll lose customers.
My guess is that in the near future American and Kayak will mend fences, and there will be some new deal cut over fees.