They seem to have clarified the controversial restrictions in the license:
IMPORTANT NOTE:
If you want to charge a fee for a work that includes files in the .ibooks format generated using iBooks Author, you may only sell or distribute such work through Apple, and such distribution will be subject to a separate agreement with Apple. This restriction does not apply to the content of such works when distributed in a form that does not include files in the .ibooks format.
...If you want to charge a fee for a work that includes files in the .ibooks format generated using iBooks Author, you may only sell or distribute such work through Apple, and such distribution will be subject to a separate agreement with Apple. This restriction does not apply to the content of such works when distributed in a form that does not include files in the .ibooks format.
provided, however, that this restriction will not apply to the content of the work when distributed in a form that does not include files in the .ibooks format generated using iBooks Author.
A big download from the App Store for just a few words in a PDF!