Most chipsets on the motherboard are encapsulated in a plastic sheath, while processors are almost always covered by a metal plate that protects the core. Such solution is used by the manufacturers to have a larger surface to install the heatsink, facilitating the installation and minimising the risk of damaging the chip.
If on the one side this protection is optimum to prevent irreparable damages during the heatsink installation, on the other side it considerably increases the heat transmission resistance. For this reason, several expert users prefer using chips without such protection and applying the heatsink directly on the core surface.
Browsing through the forums it is common to find users that have broken the core of their processor while they where installing the cooling system. This happens because the core surface is much smaller than the heatsink base and an uneven pressure while installing is sufficient to make the heatsink weight relieve on the chip edge only, thus breaking it. The core protective rubbers are especially designed to ensure even pressure during the installation of the cooling system and perfect contact between the heat sink base and the core surface. In fact, during the installation of the heatsink, the weight is first relieved on the rubber only and when an even pressure is reached, sufficient for compressing the rubber by about half its initial volume, the heatsink base touches the core. In this way, the rubbers act as shock absorbers and eliminate the risk of chipping and breaking the processor or the chipset.

CPU without metal plate

CPU with core protective rubber applied