Only the developer of an app, i.e. Apple for the iBooks app, can make it support file sharing. If you want to copy books and/or PDFs to the iBooks app then you select the iPad on the left-hand sidebar of iTunes and use the Books tab on the right-hand side to select and sync them e.g. in a similar way that you use the Music tab for syncing music.
If you have other apps that don't support file sharing then presumably they support a different transfer method e.g. transfer via your wifi network, email, Dropbox etc