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TechCrunch reported and Budget Travel confirms that American Airlines is pulling its fares out of the granddaddy of all airfare aggregators, Kayak.com. Effective August 1, you won’t see AA fares on Kayak.

TechCrunch also reports, citing “the CEO of a competing travel site” as a source, that American is “considering doing the same with Orbitz. If it does so, other airlines such as Continental and Northwest may follow suit.”

For starters, this stinks for consumers, because it’s making comparison shopping harder. Already we’re stuck comparing apples to oranges, thanks to the variation between the airlines’ myriad fees. But in the long run, I’m betting that pulling out of comparison sites will stink for the airline, too, and we’ll see this decision reversed.

The comparison with Southwest will inevitably arise. Sure, Southwest doesn’t show up in comparison sites, but Southwest customers have been “trained” for years now to skip the search engines and go straight to the airline. American doesn’t have that kind of culture built up, and it’s unlikely to go all-in toward creating such a culture at this point. Just pulling out of Kayak won’t do the trick. And worse, it’s a real pain in the butt to waste time looking all over the internet for the lowest fare. I have always disliked that about Southwest, but hey, it’s working for them. Still, Southwest is the exception — not everyone can pull off selling tickets solely on their their own. Even JetBlue caved in and started publishing fares on other sites.

American Airlines has played these games before. They once yanked first-class fares from Expedia, but came back three weeks later.

This sort of thing goes both ways, too. Notably, online travel agencies don’t claim to cover ALL the options. Orbitz, for example, limits customers’ choices in its rental car search to those companies that pay to be included.

I’m betting that American’s pullout is a bargaining strategy. They hate to pay any referral fees to sites that drive them customers, but they don’t want to lose those customers entirely. Their real goal: to negotiate a smaller revenue split with Kayak and/or Orbitz.

If I’m right, then American’s fares will be back online for comparison shopping within a month or so. If I’m wrong, then we will likely see other airlines do the same, and the business model of Kayak and its competitors is at risk. It’s not just venture capitalists who lose out if those sites fail: The consumer loses. So I really hope my prediction is right.