first off, welcome to the forums!
second, these forums are primarily for installing computers in cars, so audio questions usually take a little while to get answered...
now, onto your question-- you said it is through teh aux input-- so that means that you are using the headphone adapter right? and you are not using the pioneer ipod adapter that plugs into the bottom of the ipod?
if so, check that the volume on the ipod is all the way up, and that there is a song playing on the ipod(there is also a setting in the audio controls to adjust the input level of the aux input, so you can also try bumping that up a little)--- using the headphone jack style input, the pioneer deck will not control the ipod, only amplify the audio.