Atheists are right-- there is no scientific proof of God.
But they forget that Theology is outside of the realm of Science. Science doesn't tell us what is moral, or ethical, or anything else that may happen to be outside the realm of what science is capable of telling us.
Science is a philosophy of skepticism and empirical evidence, and as such has no ability to explore metaphysical questions, which have nothing to do with skepticism or empirical evidence, and everything to do with subjective experience.
They are simply two different, separate, and exclusive realms of knowledge and thought.
What you call "metaphysics", we call it "stuff we don't have a clear answer for yet". We just don't fill in the blanks with "Goddidit". We are patient enough to accept there's no answer for X phenomena yet. We even accept the premise we may never have the answer for such phenomena.
Everything that you know today, that you take for granted because it's so obviously true, once was considered unknown and mysterious, and thus, within the realm of the "metaphysical".
A sufficiently advanced technology is indistinguishable from a "God" or from a Metaphysical force. If you were to travel back to the Medieval ages with an Ipad and show people a youtube video, they would run away screaming that there's a sorcerer that has trapped humans inside a small, thin tablet.
In a way, the mysteries of how nature works (The electromagnetical field, the gravitational forces, the time-space complexities, the phenomena at quantum level, etc) are like a very very advanced technology that is still beyond our comprehension to grasp. Nature holds a vastly complex mechanism that we are still trying to figure out and that even as mankind goes extinct we may never fully decipher. In a way, Nature is the highest, most advanced form of natural technology there is. Like the Ipad in Medieval times (and even this comparison doesn't do justice to how far ahead of us is the comprehension of Nature in its whole). And we are the peasants, using nothing else but our critical thinking, properly mixed with imagination and common sense, to slowly, decipher the great puzzle.
So obviously, there are many many enigmas yet to decipher. And those are the ones you call the "Supernatural". But, there are also, false conclusions about what actually happened, say, when someone witnesses a phenomena they didn't understand, or they misinterpreted. Those are the Myths, which also enter the realm of the Metaphysical. So the Metaphysical is merely a cultural phenomena of men telling other men tales about stuff they have no evidence of and/or no full knowledge of.
