Is it possible manage files on an iPad directly, or do all file transfer (music, movies, etc), have to go through iTunes?
iTunes is commonly used to synchronize and manage content (podcasts, songs, videos, notes, calendar, contacts, and books) for iPad owners.
The alternative is to jailbreak which requires some technical knowledge on the part of the owner, may not have the features of the latest released iOS (it takes time for jailbreakers to release new jailbreaks), and is not supported by Apple warranty.
If you have access to a Linux machine then the libimobiledevice library is an alternative to iTunes and you don't need to jailbreak the iPad. With it, you can also mount the file directories of individual apps (whether that helps or not depends on the app). You can't add tunes to the music player, unfortunately, because the database isn't (yet) writeable by Linux tools (though if you jailbreak, you can modify the database version to one that Linux can deal with). To work with iOS5 you need the latest version (from the git repository) rather than whatever version comes with your distribution.
According to the website, there are unofficial ports to Windows.