Although I personally believe in God, your question wrongly assumes that someone or something programmed us. There is no reason to assume that.
My own thoughts are that as we become more and more sentient, we have developed a kind of God radar, a sense of the Divine. However this sense is still very primitive and inaccurate, much like an eye that can only see light and dark. This would be the reason that while religion is pretty universal, different people interpret the divine differently. You know, the old "Blind men and the elephant" sort of thing. It is also true that just as some people are born unable to hear or see, not everyone has this God radar.