to try and prove it all happened by chance.
The point of this experiment was not to disprove the existence of God, as you seem to feel.
It was designed to investigate genetic inheritance, and evolutionary pressures; to see if some of the micro-evolution we see in nature (like butterflys changing color after several generations to camoflage themselves in a new environment) could be replicated using computers. This allows millions of "generations" to be studied in a short period of time.
The results of such experiments are not pre-ordained: In the end, it is scientific experimentation that will either disprove Darwin's theory (which I happen to believe), or support its validity.
Remember how the Church forced Galileo to recant on his knees his sun-centered universe under pain of death, because scripture was crystal clear to them:Psalm 19: 4-6 says "the sun comes forth like a groom from his bridal chamber and ... joyfully runs its course; or Ecclesiastes 1:5: "the sun rises, the sun sets; then to its place it speeds and there it rises [again]"; or Joshua 10:12-13: "Joshua declared, 'Sun, stand still over Gibeon, and, Moon, you also, over the Vale of Aijalon.' And the sun stood still, and the moon halted till the people had vengeance on their enemies." Or Psalm 104:5: "You fixed the earth on its foundations, unshakeable for ever and ever."
The priests cited these verses in their condemnation of Galileo. See, they said, the earth does not move, it says so in scripture. But they were wrong.
And Galileo had no hidden, God-hating agenda. He was simply using his God-given intellect and curiosity to make discoveries about the world.
I believe most scientists today, like Galileo, work because they are curious and want to understand the functioning of the universe. They have no malicious motives, and should not be looked at with such utter distrust by creationists.