Apple has updated iBooks Author to version 1.0.1 and it looks like the major change is new language in the EULA (End User Licensing Agreement) that clarifies exactly who owns the books you create, and where they can and can't be sold, and in what format.
Shortly after Apple released iBooks Author for Mac, word started to circulate that content made within the app could only be sold in Apple’s iBookstore. It seemed like content could be given away for free, but not sold anywhere else. Here's the new language:
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.
An additional clarification derived from section 2B reads as follows:
[I]f the work is provided for a fee (including as part of any subscription-based product or service) and includes files in the .ibooks format generated using iBooks Author, the work may only be distributed through Apple, and such distribution will be subject to a separate written agreement with Apple (or an Apple affiliate or subsidiary); 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. You retain all your rights in the content of your works, and you may distribute such content by any means when it does not include files in the .ibooks format generated by iBooks Author.
So, there you have it. If you create an iBook in .ibook format, you're only allowed to sell it on the iBookstore. If you create an eBook in ePub format, you can do what you want with it.
iBooks Author 1.0.1 is a free download on the Mac App Store.