This might go without saying, but did you hit the "aux" button before or after you plugged your ipod in? i know if nothing is plugged into the jack, it won't switch to auxiliary input. If that's not the case, definitely bring it back and have them fix it.
2006 Scion tC
Unlimited Slip Differential, Custom CD's, Continuously Variable Odometer, LED LED'S, Horizontal Doors, Dead Moth in Radiator.