It has something to do with conditioning the nerve endings or deadening them. Repeated blunt force trauma to the same area causes damage to the tissue and the nerve endings in that area. Over time, scar tissue develops in that area and the nerve endings are damaged or destroyed. This makes the area less sensitive to future trauma. Still gets hurt, just fewer nerves to react to it. Over time, the nerve endings regenerate...unless you maintain the conditioning routine.
This reminds of how body conditioning can be used to develop better bones for fighting through repeated strikes causing microfractures that heal thicker and denser than before the damage. Done carefully, it's great. Done poorly, you cause lasting damage instead.
The human body's ability to adapt to whatever you're putting it through is pretty cool, imo.