The Protestant Revolution

Metaphysically, the Protestant reformation resulted in the "Supernaturalist" religious dichotomy that supplanted the older Platonic-Christian perspective with the simplistic idea of God the great artificer in the sky who creates the cosmos ex nihilo, without any mediating hierarchies of angels or celestial spheres.  .

The New Cosmology and the Collapse of the "Sacred Hierarchy"

Scholar of comparative religion Professor Huston Smith suggests that the secular world came about through the collapse of the "perennial tradition" of the "Great Chain of Being", a philosophy that had continued since the time of Plato and which, argues Professor Smith, can be found in every non-western (especially traditional) culture worldwide. It was the power of the scientific revolution in the methodology and discoveries of Bacon, Galileo, and Newton, and the dualistic and/or materialistic philosophies of Descartes, Locke, and Hobbes, that brought about the eventual collapse of the hierarchical outlook.  For "modern science requires only one cosmological level, the physical" [Huston Smith, Forgotten Truth, p.6].

However, it is clear that the rot so to speak began earlier, with the protestant reformation an dthe rejection of the hierarchical Catholic institution and cosmology. The new scientific method was only able to achieve waht it could because the groundwork has already been laid.