I've taken to using the rather nice cross-platform Clementine in lieu of Rhythmbox, which has been glitching and freezing since I upgraded to Fedora 16. However, Nautilus (the file manager) was still proffering Rhythmbox when I plugged my son's iPod in.
Under system-settings/removable-media I had “Music Player” set to “Ask what to do” not “Rhythmbox”, so I was a little stumped. gsettings list-recursively wasn't helpful either.
Finally, I remember a trick I'd had to play when I moved from grip to SoundJuicer a while ago (which I want the option of, but not for it to auto-run; grip was being offered).
You have to change the relevant setting to the one you would prefer, and then change it back to “Ask what to do”. It's sort of sticky, remembering your preferred application, even though it's not active.
Doing that, I now get an “Open Clementine” button in Nautilus when the iPod's connected.