I think because in present day, someone with Sherlock's personality would be more likely to be an atheist. In Doyle's time, Christianity was very mainstream, now it's much more of a conscious choice and very unlikely to choose for someone like Sherlock. If you look at public figures that value and promote logic and reason, you'll find atheists and agnostics overrepresented. 

I personally found the shoehorning of religion in canon Holmes pretty poorly done. He tries to use reason to explain his beliefs, but fails miserably IMHO. I don't think Moftiss could pull that off either, and I don't think they'll feel the need, unlike Doyle. 
 

Yes we are all people of our times and culture. We also may change as we age and mortality stares us in the face. Every time I watch this show I have to remember this is a young Sherlock who, like me, may go from atheism to agnosticism to believer as life unfolds.