To be honest, I feel like the distopia you are portraying is a little cliche. It's a good first draft but it reads like an essay. Try adding some dialogue, or add some more detail as to what it takes to get a society to accept fundamentalism other than "they fell back on religion".
Something more original....more dialouge...thank you for the input. Still playing with this story in my head so there will be constant changes. Not sure however, what idea for lack of a better term has not already been done to death. Or maybe I should just use a contemporary setting and just discuss what it's like to be an Atheist family in a highly Christian town.
You obviously have a lot to say about the nature of your protagonist's environment, but you don't have to say it all at once. Give us more about the man, make him real to us, and inject the info about this "new reality" as a part of his experiences. Show us how they affect HIM, show us how HE has to deal with hiding both his physical and spiritual self from all the little tyrannies in his world. Read 1984 again. Also, the world you've created might have a more emotional impact on the reader if you introduce it more as an integral backdrop to his story and less as the obvious point of the story. Don't give up, though. The world needs this kind of literature.