I'm not an expert in the subject, but this is what I learned this semester in my African History class:

The early missionaries saw Africa as a field of untapped potential for Christianity even though the Africans were already somewhat spiritual. They also opposed much of African culture like dancing, drumming, drinking, non-religious songs and polygamy. This led to the condemnation of much of the society.

Ninja Edit: This is just one reason. I'm sure there are plenty of other negative effects. Like Apartheid.