a). Do not use the words book or ebook in any part of the app or it's meta data.
b). Add native functionality that helps to showcase Apple's mobile platform.
What features you add that will help satisfy app review are up to you based on your skills, budget etc. Do something unique that makes them happy to add your app to the store.
If making a more native app is more than you can handle, you may want to take their advice and submit the content as an iBook, instead.
>Obviously, it contains other functions, but I was rejected for the following reason.
Perhaps those "other functions" were not obvious to App Review. If those other functions makes it much more than a "book" then appeal to App Review pointing out those other functions.