An atheist asks “which Supreme Being is the right one?” There is only one Supreme Being. We theists disagree on what, exactly, He is like or unlike. We even disagree on whether it is an He or an It. But we all agree that there is only one.
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To drive this point home, let’s take examples of what is usually called “polytheism”. Ancient Greek and Roman religion and modern Hinduism.
If you were a student of Aristotle and Plato in the ancient Greek world, you probably worshiped various gods, from your household deity to ones that dealt with things in your life and profession. If you were an engineer, you likely belonged to the cult of Mercury, for example. In addition to these religious practiced, you also believed that there was a distant, First Mover, a Supreme Being that created all the others through some sort of emanation, that is, the creation of a bunch of mediating divine beings.
Similarly, if you were a Stoic, you would have believed and practiced rites associated with various gods, but would have believed that Zeus was the eternal Father of gods and men and supreme above them. You would have read the legends of Zeus’s creation as the “son” of Cronus as an allegory describing how time was unimpeded, but really a creation of Zeus’s Providence as well. You may have also thought that those other gods were simply aspects of the single Zeus’s power. Zeus, in Greek, is basically the same as “Deus”, which means God.
If you are a Hindu, you believe that there are thousands of gods, but that they are all created by Brahma, or sometimes Vishnu, who “dreams the world into being”. This is a different thing than all the little gods. You may believe the little gods are aspects of Brahma or Vishnu, like the Stoics did.
Just because there are multiple views on a thing, doesn’t mean that thing doesn’t exist. It’s like saying “Which Nature is right? Quantum physics, general relativity and biology describe such different worlds!” Both quantum physics and relativity are ‘right’ in some contexts and wrong in others, the same goes for biology. Similarly, religions are right about some aspects of God and wrong about others. Us orthodox Christians believe that Christianity is the superset of all these correct beliefs, and that there is much truth to all other religions.
To use another concrete example, let’s say that you were trying to guess on whether I owned a car. If I own a car, it could be a Subaru, a Ford, a Chevrolet, or one that I constructed from the wikispeed blueprints. The fact that there are many possible makes and models of car I could own doesn’t suddenly make it less likely that I own a car, or make “Andrew doesn’t own a car” a better bet.
In a similar way, just because there are different understandings of what God, the Supreme Being is doesn’t mean that it’s less likely that He exists. The classic atheist accusation that theists believe in a “sky fairy” comes from a similar confusion between a Supreme Being and mere little gods. A sky fairy would be like those little gods that a Greek or Hindu might create a statue of. It is not the same as the Zeus of the Stoics or Brahma of the Hindus. Fairies are supernatural, but created beings that resemble humans and have magical powers. In western cultures, magical powers are those that can be commanded by human actions, appropriate sacrifices, deals and so forth. If you were to ask a student of Aristotle or a Stoic whether they could command the Prime Mover or Zeus, they’d laugh at you. Of course you can’t! The Prime Mover was totally transcendent, and Zeus was the general manager of the universe and mankind. You would pray to him, but you followed HIS commands, not the other way around.
So, the sky fairy that atheists thinks theists believe in is nothing like any conception of God, but it is kind of like a little god or magical pagan spirit. Conceptually, this is like mistaking a hamburger for a cook. What would you do if an otherwise normal adult mistaked a hamburger for a cook? You’d laugh at them. This is why we laugh at atheists who make this mistake. Now, many atheists would argue that this is a case of special pleading. Which, if you have been following along, it’s clear that it isn’t the case. A cook is different than a hamburger, the supreme being is different than a mere god.