Apple created the iBookstore and the new iBook Author tool. As creator of said platform/application, they can put stuff in their EULA that says "you must never use this tool without wearing pants" if they want. It's their IP, they can do what they want. But just because they can set whatever terms they want doesn't mean they should set unreasonable ones. To many, the "if you want to profit from this work you need to cut us in on it and you can't go anywhere else" clause is unreasonable, like the aforementioned hypothetical "pants" restriction. Personally, I don't think it's unreasonable… I do however think it's self-defeating for Apple.
The "exclusivity" clause will make creative people think twice, and many will avoid the iBooks storefront/platform all together due to it. Who does that hurt? Certainly not the creative types because they have multiple tools they can use and multiple channels to promote and sell their content (look up "the Internet"). It will end up reducing the variety and choice in the iBookstore… making users less likely to think of iBooks as the "first choice" for ebook shopping. it hurts Apple more.
I have two books available for sale on both the Kindle and the iBooks store. I'm working on two more. One of them will be available anywhere, the other will only be on iBooks and be created using the iBooks Author tool. Why? Because I am selling the first book and giving away the second, so the restriction doesn't "hurt" me…. and I don't "need" the iBooks Author tool to create my work. Would it make my life easier if I can use iBooks Author to do ALL my ebooks? Sure. But it's not a deal breaker for me.