The throwout bearing should only give you a lot of noise when it's actually in use, ie, when you have the clutch pedal depressed, not the other way around. I had a problem where if I put my car in neutral and let it idle, I had a nasty grinding / scraping coming from the tranny. It got messed up after I had my gear oil changed as far as I can tell, and it killed something on the input shaft.
I'm not saying this is your trouble, but if it's happening when you aren't touching the clutch, then I would really doubt that it's a problem with the throwout bearing.
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