In this article, PW talks (in a rather condescending way) about J.A. Konrath's deal with Amazon. What's interesting to me is that Konrath says in his blog response that all PW asked him about was his royalty: "I was contacted repeatedly by PW, but the only question they asked was about the royalty rate of the Amazon deal. I explained I signed a non disclosure agreement and couldn't reveal it. The reporter persisted, asking several times..."
It appears that what concerns the big boys most is the possibility that this sort of deal might eventually force royalty percentages up. I think once again they're missing (or deliberately ignoring) a big part of what makes this deal interesting-- the fact that Konrath convinced Amazon to sell the ebook for such a low price, which is likely to result in the ebook edition outselling a lot of New York ebooks. Such low prices would be a smart thing for NY to emulate as best they can, but I think it's already quite clear that they have no intentions of doing so.