If the books that you buy/download have any sorts of digital rights management on them then you will not be able to copy/transfer them into other ebook reader/app. From http://support.apple.com/kb/HT4059 :
iTunes can show you the kind of book you have by selecting the book and then choosing File > Get Info. If the Kind is marked as Book, this is a book you downloaded from the Internet. If it is listed as Purchased Book, it is a DRM-free book downloaded from the iBookstore. If it is listed as Protected Book, it is a copy-protected book from the iBookstore.
I've only downloaded some free books from the iBookstore, and some of them show as Purchased Book (old out of copyright classics) whilst others show as Protected Book (more recent free books). I would expect that most (if not all) in-copyright books will be protected and will not be transferable.