You shouldn't rely on the iPod solely to store music. Anyway, this ("this" being your issue) is because your iPod is set to automatically update, in which case iTunes does all the work (yes, this is highly recommended) and your entire iTunes library is synched to the iPod. If you'd like to
mess with the iPod's files yourself, set it to manual update. You can do this via the iPod preferences pane.
Also, if it's any consolation...
PodUtil
YamiPod
Both will rip files from your iPod, and place them in a specified folder on your computer.
Good luck.