After Liu Kang won MK1, Shao Kahn sent Baraka and the Tarakatas (Nomads back then) to Liu Kang's Shaolin Temples. They decimated it, leaving it in ruins, and Kung Lao was the only one to survive. Anyways, sometime during the MK3 conflict Kung Lao gained some sort of vengence, as he performed his MK2 fatality on Baraka. Baraka was not killed though, and showed up in MK: Gold with the scar from Kung Lao's attempted fatality, with staples holding his chest together from where Lao cut him.
That is why they are enemies...
(However Shaolin Monks may change all of this

)
If you wanna check it out, you can read the scene
HERE