What makes modern people 'naturally' disbelieve in God?

(My answer; speaking from the experience of several decades, in the middle years of my life, as an atheist...)

The fact that all modern public discourse excludes the divine.

As a modern child grows up, he becomes socialised, he becomes trained in modern public discourse of many kinds: school work, everything to do with the mass media, sports, pastimes, hobbies... and all of these exclude the divine.

It Just Isn't There. The lexicon of objects that function in the system exclude the divine; the causality of the system excludes the divine.

As the child reaches adolescence - these modes of thought become more dominant, and they become habitual to the extent of being simply taken for granted; and eventually they become so habitual as to be extremely difficult to break out from.

This process is exacerbated in the world of work, where nearly all jobs exclude the divine (in whatever social system, the law, medicine, science, government, politics, police, the military, engineering - as well as the mass media and academia) - becoming competent means internalising these 'materialist' ways of thinking; thus, excluding the divine.

So, the more expert I became at public discourse; from the level of everyday socialising, through my education and professional practice in science, medicine, literature, philosophy... The better I got at 'work' and interacting; the more I internalised the systems... the more adept I became at working-within and extrapolating-from the systems... the less time and space there was in my thoughts for God. 

So, modern people - after early childhood - tend to become habitual atheists at the level of their thought processes.  And this happens most to those who work in the congitive realms; and tends to increase with expertise.

And long-term, frequently practised, and socially rewarded habits can be very, very, Very difficult to break (if/ when you want to break them, which too-few do).

From such considerations, I regard modernity (with its division and specialisation of function) as intrinsically hostile to the divine; hence it carries the seeds of its own destruction.