I hope my answer won't be too generic, as I have little to no experience with iPods etc, but perhaps you might still find this useful.
The problem might be that Wine "sees" the iPod through the Linux drivers, which makes it very different from connecting your iPod through Windows or Mac. iTunes expects to see a USB device with a certain driver, and because Linux intervenes here, it will see a different one that it cannot recognise.
If this is true (and if anyone reads this, please correct me if you DID get your iPod to work through Wine), I'm afraid it will be very hard to get your iPod to work through Wine.
There are plenty of Linux native alternatives available though. For example, Rhythmbox claims to support iPods through its plugins.
If you want to read more on iTunes user experiences with Wine, try WineHQ.
Update: izx has another good idea if you want to run iTunes on your Linux machine and be able to synchronise your iPod: set up a virtual machine (e.g. through VirtualBox). If you then enable USB support you should be able to synchronise your stuff. Again, I cannot confirm this from my own experience, but it seems that izx is usually right :)
Best Answer
Rhythmbox or banshee both are very good and they support ipods and iphones.