I have the same problem, my bike sounds like it has a very aggresive cam in there.
As i have a PCV in the bike, my tuner has put some values (-8) in the first gear map, on Zero throttle, from 500 to 2000 RPM, this has made it a bit better, but not as smooth as i would like.
This is taken from the Service manual:
This motorcycle is equipped with the idle speed control
valve. The idle speed is adjusted automatically at the
specified value (1 100 r/min (rpm)) by the idle speed
control valve system. Therefore, it is not necessary to
adjust the idle speed normally.
The ZX10R - You'll go blind from over-exposure due to it's pure awesomeness!