Quote Originally Posted by Nitrox
I'd be more concerned damaging the crown when cleaning.
I agree that damage while cleaning is a concern. However, the original question dealt with the reason one might cover the muzzle of the rifle, so mentioning other mechanisms that might pose a greater risk of muzzle damage, while useful information, does not answer fly223's original question.

Having said all of that, damage to the chamber and crown while cleaning a bolt gun can be mitigated by always using a bore guide, using a good, one-piece cleaning rod (I like Dewey rods, but there are others), always inserting the rod from the chamber, rather than the muzzle, and removing the cleaning jag from the rod so that it does not damage the muzzle as the rod is drawn back.