When you create a cover for your fixed format ebook, the cover will only be visible in the iBooks library. It won't appear in the ebook itself. When you click on the thumbnail of the book in the library it will open to the first page of the book and not the cover.
This is due in part to requirements by Apple iBooks Store. As a workaround, you can create a new page at the beginning of the book, then re-create the cover content on that newly created page. The "cover" will then be visible as the first page of the book.