The point of linking to Amazon is to sell books. Sure, they can sell books through independent book stores. The question is: do they sell more books by linking to Amazon (a recognized brand) or an independent (which the potential buyer probably won't recognize)? Something tells me they will sell more through a recognized brand, like Amazon. That's particularly true for physical products, where you may be left hanging for several days with nothing better to do than wonder if they're a reputable vendor.

Then there is the issue of compatibility with ereaders. From what I've heard, anyone targeting the U.S. market is going to have to sell in a format compatible with Kindle. If the author or their publisher insists upon DRM, that means you're going to have to point them to Amazon.