The same problem exists with the new Google ebooks service.
I back up my computer with Time Machine and Carbonite. I'm not worried about losing the ebooks stored on my computer. I don't need Amazon or Google to "keep my books safe."
Compare to O'Reilly Media: "Whenever possible we provide [eBooks] to you in five DRM-free file formats — PDF, ePub, Kindle-compatible .mobi, DAISY, and Android .apk — that you can use on the devices of your choice." (from their website)
Music from iTunes is similar to eBooks from O'Reilly: no DRM, download the files and store them yourself.