Probably the bit about how they can't distribute it with DRM and must allow people to easily copy it from that point of distribution. I don't know for sure how free kindle e-books are distributed, but my gut tells me that it's the same way that non-free e-books are. If there is DRM preventing me from copying that e-book to another device, modifying that e-book, etc, then it would be in violation.
The fact that it's a settling doesn't solve the problem. If they decided to build whatever infrastructure was required to flag copyleft content and then essentially lock this setting, they might be in a better position. It still doesn't protect them completely. If the author fails to include the license in the book, for instance, they're in deep water. So the important thing to remember is that they can't get into this game lightly. It takes a bunch of work.
The GNU licenses are not designed to facilitate maximum spread of the content. They're designed to enforce sharing. Unless Amazon wants to get involved in that enforcement, they really can't touch this stuff.
