I think I understand you.
A longing for something beyond this reality and a deeper understanding and relationship with pure love, compassion, understanding, mercy (which is what God is -- the absolute Truth of all things in conscience form), and truth is natural. For me, this is overwhelming proof that these things exist and can't be explained away by natural processes or chemicals in the brain.
People doubting they have a soul and a spirit which lives on if found pure is definitely an idea that has only become popular in modern times. But this isn't due to us becoming smarter and more intelligent. The most brilliant men of our past who were giants in their fields, and continue to stand as giants today, because their work and ideas are still relevant today, and touch on deep understandings about the nature of man and reality.
The best men this world has ever produced were devout men of truth who had deep religious convictions which inspired their work and motivated their intentions.
Anyone who thinks they are better or more intelligent than someone merely because they do not believe there is a cause for our existence is treading on the heights of hypocrisy.