Very good point. If Apple had wanted it to be possible for third party developers to make software to interact with the iPod then they would have published the interface one should use. The fact that they have not implies that they don't want this to happen. This next step is an obvious extension when they saw that despite the lack of a published interface, others were still making third party software.
When buying such a device, the onus is on the purchaser to decide it's suitability for their intended purpose. The onus on the vendor is only to make sure it does what it is described as doing. Therefore, if you want a media player to use together with Linux, or if you want one to use with Windows or Mac and do not like iTunes, then probably the iPod is not for you.
Having said that, if I only purchased hardware that stated it would work with Linux, I would probably have no hardware at all.... so we really are between a rock and a hard place here.