Before Darwin, no one could come up with credible way that complex processes could arise spontaneously out of simple processes. All people had observed were things breaking down into components and the increases in entropy or disorder that we all see in everyday life. Only creations of human intelligence and life itself would appear to break this pattern and create complex processes. The argument that if you observe a watch, you can safely say that a watchmaker is not only possible, but certainly existed was very difficult to answer. In fact it could not be answered based on the science of the time.
And yet, in spite of all the scientific evidence there were those with enough faith to believe that there was no god. Eventually, Darwin gave their faith more intellectual cover, but surely the amazing faith of the atheist is something that Christians can recognize and respect.
Of course, the belief that atheism is somehow "scientific" or supported by science is nonsensical. To try to take physical phenomena and disprove that it was created just doesn't make sense. Whatever you can prove about the nature of the universe has no bearing on whether the universe is created or emerged without creation. You can perhaps prove that God didn't leave obvious "fingerprints" on the universe. That may reveal something about the nature of God and his relationship with man but nothing about His existence. The atheists have their faith, the religious have another.