The protagonist Miles doesn't really portray why most people turn to atheism. It is not a trauma in their lives that makes most people atheists, but a general lack of evidence of God that makes most people leave religion.
Plus, I do think that the writers will never be able to explain how the God account is working. It will be too detached from reality if it turns out actually the account of God. (Ignore the question: Is he the Christian one or Hindu one?) It will fire up the religious viewers if it turns out that it is just a miracle of technology. I feel like the writers will have to conclude the show in an open-ended fashion, like a dog-whistle to religious people that it was actually God who operated the account. I feel, in doing so, they will be cheating us all.
This show would be far better if it were like a sequel to Person of Interest.