One of the wisest things I have heard on this subject matter is this:
"The worst prejudice of all is to think that you have no prejudices."
Everyone has prejudices, whether they come from their religious beliefs, upbringing, other experiences, or anything else. The human brain cannot contain so much information that we can put ourselves in the mindset of everybody else. Prejudices are a negative form of the simplifications of the world that we need to make in order to sort our thoughts and experiences.
I am a Christian and believe in an almighty God, but I believe one of the great good things He gave us was our free will. We can thus choose which paths to take in life. I also believe that God created the Universe in such a fashion that there are chances and probabilities, nothing can be foretold with certainty. (If God would create a universe that was completely foreseeable, how much fun would He have observing it?) Among the chances and probabilities are the mutations driving the evolution forward. The chances and probabilities are also the foundation for the free will, because we would not have a free will if everything was predetermined. The chances and probabilities are thus, in my mind, a blessing but often also a curse.
There are some people, mainly extreme feminists, who claim that the differences between the sexes is entirely based on society and the upbringing. I do not believe that. The fact that there are people who feel that they are born in a body of the wrong sex disproves this feminist theory.