The store will get a portion of Amazon sales but only those that take place through its in-store networks. It will also get the benefit of some Special Offers on the ad-supported Kindles, and have some kind of Read For Free plan in which, presumably, Kindle owners can read certain Waterstones e-books free in the store.
Amazon already sells its Kindles through a number of other UK bookstores, so perhaps Waterstones figures that if you can’t beat them, join them. Daunt made a number of other remarks at the meeting according to FutureBook. He didn’t think most Waterstones customers would actually care that the store sold Kindles, for one thing, and that the partnership would continue for as long as it was beneficial to Waterstones.
At any rate, businesses will happily make deals with other businesses if they think there are more benefits than drawbacks. If Waterstones thinks Kindles can draw more people to its stores, more power to it. It remains to be seen whether or not that will actually be the case.