The Moderns criticized Religion for its obsession with the invisible. Where is God? Who has seen him? Is it rational to accept the existence of things you cannot see? Then they went to work, relying on instruments like microscopes and telescopes to establish the existence of things they could not see.
The Moderns criticized the doctrine of salvation by faith in things unseen, then developed a germ theory of disease. Later, the Moderns criticized the doctrine of original sin, then sought to identify the neurological origins of antisocial behavior. Later still, the Moderns criticized Religion for its fixation on a bodily resurrection, then proposed cryonics as a worthy field of medical inquiry. Recently, the Moderns derided the concept of an eternal soul and End Times theology as the province of the fool. Then, they pledged an historically unprecedented amount of capital to develop artificial general intelligence, while positing a fast approaching and inevitable technological singularity that will bring about the end of human existence as presently conceived.
The Modern challenge to Religion is traditionally understood as a conflict between faith and reason. It is better understood as a turf war. The turf is a common set of questions of existential consequence. The war decides whose answers to those questions get to matter.