The religious authorities used to have a monopoly on truth, and their explanation of the universe, taken for granted as a principle, was the basis for their power. If their explanations (e.g. the earth is in the center of the Universe, early and Middle Ages Christianity) would be proven to be wrong, their power could be questioned.
The Scientific Revolution questioned many of the older beliefs, and provided new explanations, supported by evidence, hence being a threat to religious authorities.