How long has it been since the download? I'm pretty sure that if you have an iTunes account set up (which you have to) then it should be automatically charged to the account linked to iTunes, be it credit card or store credit. I would give it a little while longer because it might take longer to actually process the purchase since it's not "directly" from iTunes itself.
I haven't tried this but I did also read that if you remove your CC info from your iTunes account, and have a Gift Card balance, that any Wifi purchase would then be deducted from your Gift Card. I'm told it works but I can't confirm.