I researched this issue and discovered that some library downloads are wma and iPad doesn't use wma.
In my library's website, they actually provide users with a category that specifically lists books that are all iPad-friendly, eliminating the need for me to have to make sure I'm not choosing a wma book.
Also, the library's website should give you the directions on how to do the downloads specifically for iPads - at least it seemed pretty straightforward to me.
Good luck.