In reading this article, it's clear that Apple are effectively shutting out Linux users from using the new iPods. There is currently no iTunes for Linux, and no signals that one will be developed in the near future. They have changed the structure of how the iPod works, encrypting the database with a hash that ties that database to the iPod.
My opinion is this: that Apple should be more platform friendly towards Linux, especially with it's iPod support. Look at Adobe releasing the Flash plugin for Linux, as well as Microsoft's Silverlight plugin. Bring out an iTunes-light for Linux, make it open-source, let the Linux community manage it themselves. Sure, people will know the inside of your software, but rather have it this way and control it, than have some person reverse engineer it and you're left with the impression of being the big bad guy.
Maybe don't even make it open source, but release a core linux version with an API, and let the people build it.
You successfully took the digital music arena, which was a mishmash of illegal copying, file sharing, etc - and made a very lucrative business model from it. I'm sure you can do the same in this case if you apply yourselves.