Currently there is no linux software (or library) that can successfully read, write and update an iOS device's music library running iOS 5 or higher. All applications (that I know of), are dependent on libgpod for this functionality and libgpod has not worked properly with the current versions of iOS for some years now, ever since the database version (DBVersion) of the iTunes library within the device hit version 5.
Your best bet right now is iTunes via wine.
Thanks to kracheck, member of kubuntu Forums (www.kubuntuforums.net) now I can transfer music from my Ubuntu 12.04 laptop to an iPod Touch 4g, running iOS 6.3.1 using File Manager app on the ipod (from TapMedia Ltd.) which is a free app and has an integrated player (right, I'm not using the native "music" app on the iPod, the music database is empty there).
Here are the steps:
On the iPod - Install the File Manager (from TapMedia, Ltd.) app
On Ubuntu:
sudo apt-get install ifuse
sudo apt-get install ideviceinstaller
Thats it, I connected the iPod to a USB slot on the laptop and Nautilus launched, showing the FileManager app icon. I selected the icon and that took me to a "Documents" folder, went to that folder and then from another Nautilus windos I only had to drag and drop my selected songs (I had to go up one folder and went back to Documents to see fhe file, if you stay there after transfer completes, the file is missing, if you go up and back the files are there)
Unmount the device, go to the FileManager app on the iPod, go to Documents folder and your songs are there. Select a song and tne included player starts playing the song.
Best Answer
It is not yet possible to sync with devices on iOS 6.x.x. In fact, libmobiledevice still does not support syncing with iOS 5.x.x
See here : How to sync songs in Rhythmbox with an iPod