Congo used to be the private country belonging entirely to king Leopold II of Belgium, who was the founder of "Congo Free State".
Congo Free State was solely meant to increase Leopold's personal property, as the land *belonged* to him personally. The para rubber tree plantations and ivory were the main goods delivered from there. Leopold's Congo is infamous of the treating of local poplation. They were quite ruthlessly enslaved and forced to work at forementioned plantations in miserable conditons.
Death tolls estimate in millions. The population was kept under control by mass murders and other atrocities. More very fun reading found in wikipedia article of
Congo Free State.
I would still say that most genocides and, should we say, violent endeavours in the history of human have originally been motivated by greed and in some occasions, expansionism, which is after all only one form of greed (more land needed to maintain the economical growth, like in Rome). Of course colonization was the culmination of this behaviour.
Many leaders have used religion and help from religious authorities to help controlling the masses and giving superficial justification for their actions. For example the conquistadors were *supposed* to convert pagans into christianity, but mostly they were there to gain profit, for themselves and to their countries (Spain and Portugal, at this stage). Later on, Great Britain joined the club, partially because colonization was as good economically as it was bad morally, and partially because not entering the colonization process would've handed the world to two other super states of the time... but that's all getting a little distracted.
Shortly - in most cases, religion has been only superficial motive, and the actual driving force behind the atrocicers (is that a word?) has been personal advantage.
Even the crusades fall into this category, if you look deep enough. The crusaders consisted partially of criminals and vandals who "earned salvation" - ie. avoided conviction/execution - by joining the Armies of Light against the heretics, and partially of warriors who had no wars to fight.
The reasons for why the catholic church organized the crusades in the first place was mainly this: The Europe was full of people with warrior origins and culture (vikings, magyars and slavonic tribes, to mention some) who had invaded the lands... after the Roman Empire was divided and the Western part was screwed... Now, these people with warrior culture didn't have much to do, so they mainly caused havoc and destruction around different areas of Europe. The church had very little luck in trying to stop these violences.
So, when that the Byzantine emperor asked military help from the catholic church, they were more than happy and able to get rid of those ravaging barbarians and send them away to distant lands. Then it became an institution, and institutions don't need reasons.