It seems unusual that Ubuntu mounts your ipod without giving your rights to make changes to it. I'm pretty sure that doesn't happen on my PC.
Have you tried using rbutil to do the Rockbox installation ?
In any event though - you should be able to delete the ipod's content by doing this :
1) Figure out where your ipod is mounted, it's usually "/media/"
2) Launch a terminal window.
3) Type "sudo bash", and enter your password when it requests it.
4) If you want to *completely* remove all your current content from your ipod do : rm -rf /media//*