good question, and kinda hard to answer. there are many different dynamics to this era and what were motivations for colonization. obviously the european powers sought resources from other distant lands, such as sugar, silver, spices etc. but in terms of what the colonizing powers view was towards the native inhabitants of a given people vary by time and place.

there began to be a significant amount of chatter among the european scholarly class around the time of this fellow here:

http://en.wikipedia.org/wiki/Fran%C3%A7ois_Bernier

pretty much he is one of the first major european thinkers to officially put into print the theory of dividing different humans into separate sub species. this is in the mid 1600's. pretty much he was a traveler who kept journals of his journeys and sold his personal memoirs to the public back home in france. his first writing using the exact word "race", was him implying there are like 4 or 5 different kinds of races. and in this memoir, he pretty much talks about women. like his own sexual preference, and which race he thought was hotter than the other race, and which race he thought didnt have hot women etc. and yes, im being serious, its a short read but it got a lot of attention back in the day. so pretty much we are still using this word "race" that was coined by a horny french guy some 300 years ago.

after this article was published, other famous scientific scholars at the time began to come up with their own theories of race or "types" and other names to classify human beings by. a lot of literature started to spread about this. and many studies involving human bodies were involved at times. especially of interest were human skulls. trying to figure out who is the smartest by the size of the cranium.

fast forward to darwin, who started to figure out about evolution and all sorts of crazy radical ideas about evolution and cross breeding etc. you had people who began to bastardize his discoveries which led down the path of eugenics. eugenics really got A LOT of attention, because this was a time when various european powers were colonizing much of the undeveloped world.

one thing you might find interesting is this great documentary about shark island in namibia and the second reich operating in namibia. this has a lot to do with colonization and brutal experiments on humans subjects at shark island, along with the backdrop of many of the young officers in the second reich becoming future leaders of the nazi's third reich in WW2.http://www.youtube.com/watch?v=A0iUhTFFYTw

iin general, the theory of race evolved substantially within a few hundred years. i think that it was a justification to dehumaize other conquered peoples, but i dont think it was a primary motivating factor in conquest. there is so much history, and different scenarios during european colonization, along with different policies governments implemented that varied greatly over times. so i cant really answer a question that broad, without giving you a broad answer.

but i think it can be said in most cases racism, subjugation, brutalization followed many conquests in any empire. but i think european colonization in a time of the scientific eugenics boom set a different tone for the relationship between the conquerors and conquered people.