Apple updated the iBooks Author End User License Agreement (EULA) today to clarify who owns what when a book is published using the Mac application. TUAW gives a very clear explanation:
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.
Basically, Apple owns the format, you own the content.