By default Gtkpod uses xmms to try and play songs from your Ipod, a few linux distributions come with xmms. If yours came installed with it first remove it as it does not play music from your Ipod. Then go ahead and install
xmms-mp3

You should now be able to play music from your Ipod with Gtkpod. Although xmms is not the latest player I like it because it’s small and lightweight.