Can you please elaborate on this? Do you mean that Apply is paying some kind of affiliate fee? And what happens if the app is free of charge (FOC)?
iTunes affiliates get a cut of 5% of all purchases within 72 hours, not just for the originating app (or media).
Aren't most of the apps that AppGratis links to discounted to free for the day. Apple doesn't pay commission on free downloads, right?
Affiliation is not limited to Apple App Store, affiliation exists also on Amazon for instance, but not on Google Play, for the moment.
It's important to note that you can becomes affiliate even if your send a customer to the App Store with a free app (for instance Angry Birds Lite), and that at any time there is only one affiliate by device: that's why any apps recommendation will send you push notification each day to remain the current affiliate. And affiliation is not directly managed by Apple but by LinkShare for US, and TradeDoubler for Europe.
A last thing, doing affiliation is really easy:
https://itunes.apple.com/us/app/meon/id400274934?mt=8 => a link to my app without any affiliation
http://itunes.apple.com/us/app/meon/id400274934?mt=8&par... => a link to my app with Linkshare identifier (partnerId=30) and my company identifier (siteID=pPE4bVE6DtE)