I had a similar problem with my phone and its charger. MyLink would try and get data off of my phone, but with it being dated and all, would come up over and over with "Unsupported Device" notification. Easy fix, I cut the data wire on my charger so that there was only a ground and 5V. You could do the same on an aftermarket iPod cable, although you could only play music via Bluetooth/AUX. The other suggestion may be using the cigaret lighter socket, but believe me, I know you'd rather have the USB cable neatly hanging from that glove box through that nicely purposed wire hole than to have wires and adapters dragging over the center console.
*No disrespect, mowcowbell is right about the 12V adapters charging faster, that is a perk I forgot about.