Sounds like you have the firewire hard drive mode enabled. Firewire hard drive mode is for if you want to back up your files to your iPod. Also, you can drag text documents to the Notes folder on the iPod, a new feature.
You can do one of two things. If you want to keep your iPod in Firewire hard drive mode, just go to the Finder and drag the iPod icon to the trash bin, this will disconnect your iPod and then you shouldn't see the "do not disconnect" message. Also, if you click on the iPod button at the bottom left hand corner of iTunes (when your iPod is connected), you can change the settings and unselect the Firewire hard drive mode (which is what I ended up doing - I'll just enable it on the occasions that I want to copy files over).