If the noise is there with the clutch pedal not pushed in , it is NOT the throwout bearing, as it only engages and causes issues when the pedal is pushed in, releasing the clutch.
The noise you are hearing is an input shaft noise, and it is a fairly common issue. I have an 06 TJ with the 6 speed and is rattles pretty bad in neutral also, but I can push the pedal in and it goes away. Its just the nature of the beast as I have tried various combinations of fluids to get rid of it. Its a jeep thing..