How can atheists not believe in the supernatural when the universe is supernatural in itself?

Judeo-Christian Theology and the Islamic Faith all is symbolic ancient writings, and I know for a given that Judeo-Christian Theology, if interpreted and studied correctly, we can find great cosmological discoveries similar to the Renaissance where tons of scientists who were believers amazing discoveries. For the Islamic Faith, it sort of follows certain aspects of Judeo-Christian Theology but I'm afraid that Muhammad on some of his understanding is flawed. There is a strong possibility that Muhammad is indeed a prophet, and was called upon God to give the good news, but somewhere down the line Muhammad misinterpreted the messages. Anyway how can an atheist not believe in the supernatural when the universe is supernatural in itself? Everything that we come to know about the basics of the universe came from the Holy Bible, and by Christian thinkers who interpret well; they saw it as symbolism which is the key to understanding historical text.