Atheism is rejection of faith
First your question is wrong in that it assumes atheism is about the rejection of god/gods/spirits/supernatural creatures. It is not. A-theism is the rejection of theism. Theism in turn is the notion that a human being can know the mind of god(s), and that this human therefore commands higher influence in public discourse.
...or shortly put: atheism is telling the one that claims to speak for god(s): "No, you speak for yourself and other humans that share your faith".
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If by "atheism" you mens something else in your questions, then please specify that in the question so we know what you mean when you say "atheists".
But let it be known that if by "atheism" you try to attach anything that can be construed as unreasonable, irrational or outright idiotic to the term, here you have at least one atheist that will tell you that you need to label that as such and not "atheism".
If there is one thing we as atheists — in general — pride ourselves in it is rationalism and adherence to observation and deduction, no matter what the conclusion is.
Belief in contradiction of observation, or — as is most often with religion — in absence of observation, is what we oppose.
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So how do atheists react when suddenly miracles start occurring? Exactly the same as before: rejecting the human that claims to know on faith. They will however listen to the one that brings proof, or even better yet: hear it from these creatures themselves.
Do note though that miracles are not proof of divinity, truth or righteousness, nor do they command reverence, obedience or worship. Before any such notions we will want to have a long good chat with these beings and have their viewpoints on morality and ethics. And if they try to push us around with commandments that do not sit well with our sense of right and wrong, you can expect there will be trouble.
And why so? Why does the supernatural not command reverence? Because you and I are supernatural, in the eyes of pretty much everyone of our ancestors a mere 200-300 years removed.
You are dying of a wasting illness that makes your flesh fall apart for no apparent reason? Behold, I give you this greenish-yellow fruit from Persia, that tastes sour (but goes well with gin). Eat it, and your malady will be cured. How it works? Oh it simply makes it so that your body does not melt itself from its own body heat.
Gather around all ye, and watch how I — with this water wheel, some copper wires and a metal core — create a magical force that can create light in the dead of night as if I had harnessed lightning in a bottle; that can make your millstones turn without either thrall or oxen touching it; that can melt metal in an instant either fusing it or making it split apart; or even kill you horribly as if you had the fires of hell coursing through you!
Look here... now smile! Look, I have captured your likeness in this strange device. And not only that: it can capture your motion and your voice as well and repeat them verbatim to you.
The smallest child today can affect "miracles" and feats that even the most learned of days past could only dream about. Something as simple as being vaccinated, and thus untouchable by smallpox, tuberculosis, polio, would appear as totally miraculous by our ancestors. To us, it is an annoying prick in the arm and a swelling for a few days.
So if by some happenstance we are suddenly plonked down in ancient times, would it be wise for those people to start worshipping us and obeying our every command, just because their priests/shamans/elders tell them so? Of course not. we are still no more than human... worldly, earthy and just as flawed as before.
Atheism is the rejection of all those that try to elbow their way ahead in the public discourse by saying "I have faith that I know the mind of these supernatural entities, so you must obey my commands". And that does not change when supernatural things start appearing...
...as popular culture has long since proven: