It is a natural and normal thing to do. As you have seen from some of the other replies many overcome this guilt-ridden concern about masturbating.
My advice is to make sure it isn't affecting him too badly for too long. If he doesn't grow out of this after realising that it is perfectly acceptable and natural then try speaking with him about it.
~ The journey of a thousand miles begins with a single step ~
* Nothing in the world has ever been accomplished without passion *