Being a tool that creates iPad-only stuff isn't the problem here.
Apple says "We can refuse to put your book in our store", "If it's in the store, we can take it out whenever we want" *and* "We are not responsible for any loss you may suffer because of it" *and* tell you at the same time "If you used our program, then you are not allowed to sell it anywhere else"...
If you're all fine with such draconian conditions, then I give up.
Please write a book (or a multimedia application, however you want to call it), using iBook Author. Put it into the Apple store. Create a complete company out of it that provides for your entire income. You would not be the first to do anything like that.
Then see what happens if Apple does not like you anymore for whatever reason.
And don't say it will not happen.
Google has been dragged to court, because they merely changed their pageranking algorithm; which caused companies to drop off the first page of the search results, losing most of their revenues.