Unfortunately, that is something we can't help you with. Apple has designed the iPad to, essentially, be a one-person device. So, there are no provisions on a stock iPad to make apps (like iBooks) private.
Now, if you were to jail break your iPad, you could install a tweak to let you password-protect the iBooks app (but not the books themselves). Again, however, you have to be jail broken; this is not possible on a stock iPad.
Sorry.
Marilyn