The noise you are experiencing is affectionately referred to as "Getrag rattle" in older BMWs. Basically the input shaft/layshaft bearings of your transmission have wear in them and when unloaded and spinning slowly (idle) they will rattle around a bit. The problem is exacerbated by a lightweight flywheel in that it provides less of a "damping" effect that would attenuate the noise.
When you press in the clutch it goes away, because the input shaft and layshaft are no longer connected to the engine and no longer spinning. It is NOT the throwout bearing as the TO bearing is only in action when you are pressing IN the clutch.
It happens on most old(ish) manual transmissioned BMWs. My 330 6 speed does the exact same thing, as well as my E30 and most other BMWs I've driven although some are louder and some are quieter. My suggestion would be to learn to live with it, unless you want to tear your trans apart and replace the bearings. A heavier flywheel would also help quiet it down a bit.
Last edited by Wh33lhop; 10-10-2012 at 04:10 PM.