You own a car, but you're licensed and registered by the state. You can paint it whatever color you want, but can you make an exact duplicate of that car and sell it as your own? Nope. Can you sell it without transferring registration? Nope (at least, not without alternate state paperwork). You might "own" it, but you still can't do whatever you want.
You're licensed iBooks Author and you enter into an agreement. You create, retain copyright, and own the product, but you can't copy it and do as you please. You follow the licensing and only have certain rights when it comes to the .ibook file.
A comparison in my mind would be saying GarageBand creations can only be sold through the iTunes store. The difference I see is that iBooks Author is not outputting a simple media file, but a more complex experience filled with medias. As often the case with Apple, they want to lock that experience (& resulting profits) into the best device for it, the iPad.
hm, you may be right. I got it from the paraphrased part of the article (right after the bold EULA text) but now that I look at it, it wasn't actually stated explicitly in the contract anywhere.