A female rabbit will often pull out her own fur to make a nest when she is pregnant, or having a 'phantom pregnancy'.
However, if you're certain he is a boy, it could be that he's in moult. I know it sounds crazy, but at the vets I'm currently training at, a boy came in who pulled out his fur at the start of every spring which was put down to moulting.
And one more suggestion, does he have many toys? And if he does, does he play with them? He could be doing it because he's bored.
Obviously I'm only making suggestions since I haven't seen him, and it's probably best to get back to your vets in case there is maybe a skin problem there!
Sorry for such a long post!