I had the same problem. When that cap is missing it actually creates and intake leak! I was told (from someone on this site) that a good backfire can cause the cap to pop off.
Although I did not recall a backfire at any time on that bike, I took the advice about replacing it and using a small black tie wrap to secure it. Never been a problem since then.
Mine was idling funny and dying once in a while as I pulled up to a stop light. After replacing this rubber cap, I still had the funny idle symptoms. I then started the bike cold and let it sit and idle all the way to hot idle temps on the motor WITHOUT touching the throttle. This allowed the IAC to recalibrate itself all at once, and cured all symptoms. The reason I did this was because the IAC had gotten itself trained in an attempt to keep the bike idling properly with the intake leak.
I probably could have just ridden it a few times and it would have retrained itself, but by letting it idle from cold to temp without touching the throttle it did it all at once.
Bike has not died at idle once since then.