Many people are vehemently afraid to acknowledge this, yet the fact is that religion is what has fueled racism. Religion was born of a man trying to convince everyone in his group that he deserved all the wealth and power, by using an invented illness and offering an imaginary cure.
But the followers would soon have nothing more to offer, do these men then used the fear of the unknown to convince the followers to take what the people who were not like them so they could pay for this cure. This would still cause the resources to run out, so the men also needed to convince the followers to make more.
Thus they convinced the followers force those who were not like them to do the work, by now the leaders had to convince the followers they were special. Now we have the subjugation and slavery of anyone who looked different, what we call race.
This is the birth of racism, in reality the birth of all prejudice. Today it is fueled by the religious beliefs, us versus them and invented illnesses called sin.
The disconnect is actually cognitive dissonance appearing. Even those who, like me, just don't accept the myths of religion are often scared to accept all the problems perpetuated by the myths.
This is because religious dogma has infected our cultures so thoroughly that we become uncomfortable facing it. We become dangerously complacent, and thus complicit, when faced with these facts of the matter.
It is not that religion is the only cause, it is that religion is the ones cause that can even convince intelligent and sane people to behave as if ignorant and insane.