When I was using Ubuntu as my primary OS and using an iPhone, I had to create a VirtualBox VM running Windows XP so I could use iTunes for phone management (including music syncing, since it was never smooth on Linux). You might want to consider something like that... you could map your Linux music folders onto your Windows VM through the VirtualBox software, and copy them from Windows using the VirtualBox USB mapping.
Otherwise, I think you're SOL unless Ubuntu handles MTP... which it may do in theory, but putting it into practice is something different altogether.