Because religions put him/it/they/etc into a box. They define the entity and have stories. But the stories don't add up to our limited minds. Secrets haven't been revealed to many so faith is all that anyone has to go on. And those that have the secret code can't seem to get us puny minded folks to comprehend to just believe, trust us.
Many don't deny. Many chose to not say the bible is got it all correct. That is nothing more but stories of an ancient civilizations and their struggles with life. It changes at the NT.
Just to add a little to what you are saying, if there is a god it very well might not care about peoples faith or lack of it. The OP mentioned gods light shining through their souls (derogatorily to be sure but I will ignore that) and if that is so god is evident in any good works they do. Even if they choose to not see it. The idea that an atheist is not capable of good is simply ignorant. Everyone would be better served if we all followed the best examples of how to live in this life, rather than being preoccupied with the after life or a god who rules it. In the most important things believing in god is secondary.
