The iBooks Author 1.01 is out with an updated EULA, clarifying what Apple has and doesn’t have rights over.
The change is an important one though, clarifying that Apple has rights over the format a book is in, not the content. If someone wants to charge a fee for an .ibooks formatted file, that document can only be sold or distributed through Apple, and that work will be subject to a separate agreement with Apple. The restriction does not include works distributed in non-.ibooks formats (such as the Kindle,) as TUAW’s Erica Sadun previously discussed.
Hopefully this’ll clear up any questions about Apple’s intentions.