I upgrades my iPod Touch (4th gen) to iOS6 and since then, Wi-Fi sync with iTunes no longer works. I tried resetting my settings on the iPod, as well as uninstalling and re-installing iTunes, both to no avail. When I check "Sync with this iPod over Wi-Fi" in iTunes, it doesn't show up as enabled in the iPod's General Settings. I update the iPod frequently with the latest podcasts, and my sync cable's in my car because my iPod connects to my car stereo through it. It'd be rediculous to get another sync cable when it should be able to connect and sync with iTunes wirelessly.
I have noticed a WiFi sync quirk associated with IOS-6. The computer's iTunes will recognize my iPod only if it is NOT connected to a charger. My iPad is original and is still on IOS-5. It functions properly.
Disconnect the iPod from your charger and try again. Exit iTunes and re-open it.