That's unfortunate for Linux users, because it's clearly not worth it to Apple to build a version of iTunes for GNU/Linux. But, you know, the iPod also doesn't play ogg files. So what are Linux users doing buying them in the first place?
Your argument about self contained would be good, except that it's not a case of apple not supporting other things, it's apple deliberately blocking them.
How many hacks that muck around in Apple's UX space do you think it would take for Apple to just sort of turn a blind eye to, before users starting accidentally wiping their iTunes libraries or bricking their iPhones? And how many proponents of said hacks do you think would argue that's an acceptable state of affairs?
Bad metaphor. Suppose I lived in a world where, if my TV malfunctioned, it could break my phone and my web browser, send random emails to my relatives, riffle through my address book, and delete all the music I've bought over the last five years.
Oh, and there are international criminal gangs who employ networks of botnets to attack my TV every fifteen seconds.
In that world, I'd see a real use case for the steel-cage-equipped TV.
Apple should simply ignore it: don't support it, and don't block it.
(I should note, by "you" I mean "Linux fan who bought an iPod", not "you, tdavis" :). I didn't even consider an Apple product when I was running Linux because I knew it would be too much of a pain.)