I doubt it's due to the Creative Commons nature. Amazon allow publishers to sell non-DRMed and creative commons books on the Kindle Store, and have done for years.
UnglueIt could cut Amazon out of that entirely. Rights holders would get the money directly and Amazon would get jack. May be it isn't about that but they would never admit that anyway so who knows.
Lots of self published authors use creative commons work as a cover art, so it even can be creative commons licenced.
Many books are sold on the Kindle Shop without DRM. Some large publishers (e.g. science fiction publisher Tor) is selling books on the Kindle Shop without DRM.