John Lennox, professor of mathematics at the University of Oxford, often uses a particular analogy when discussing the existence of God and miracles. I’m going to adapt it and hopefully lend some insight.
Let’s say that I put a ten dollar bill in the glove compartment of my car. The next day I put another $10 in the glove compartment. A day later, I open the glove compartment to discover zero dollars.
Have the laws of mathematics been violated? Is $10 + $10 = $0? How about the laws of physics? Might the bills have spontaneously disappeared? Or have the laws of the United States been violated?
Of course you immediately know which one of these it is, but how did you arrive at that conclusion? You assumed that the laws of mathematics and physics are valid and that the glove compartment is not a closed system. Therefore, someone must have taken it.
When Peter saw Jesus walking on the water, what should he have done? He knew the law of nature that person sinks in water. This was an undeniable fact. But he also knew that the lake was not a closed system. Because the law of nature was not violated[1], an external force must have acted upon it. Is it such a stretch that the creator of water might be able to do such a thing? Of course not!
When the naturalist/materialist atheist rejects miracles, what he is doing is accepting the laws of nature, but rejecting the open system and thus any possibility of a creator. There is no reason besides a personal philosophical presupposition.
Let’s be very clear: belief in a creator is not a violation of any laws of science, it is a choice to treat the universe as an open system.
When a scientist is faced with an apparent contradiction to the laws of nature, they do have another choice: to claim that the evidence is invalid. The natural consequence therefore is that because the universe is a closed system, then the evidence must be faulty. In this way, the atheist can, quite conveniently, reject all claims of miracles automatically without addressing the evidence at all. This is nothing more than intellectual dishonesty.
If one did not assume a closed system, then miracles could be treated on their own merits as evidence for the creator. And so they are for many people. Alas, the very evidence that an atheist requires to prove God’s existence is the very evidence they cannot consider by their own assumptions.
I don’t expect this to sway anyone, and by all indications it rarely ever has. But hopefully it will help clarify the assumptions and issues at stake and why you see the reactions that you do from those who reject both a creator and miracles.
[1] A law can only be violated if the law applies. If my wife took the money out of the glove compartment, then no criminal laws were broken. Similarly, if the creator intervenes in his creation, no natural law was broken. A law of nature is merely a description or explanation of observations, but there is no scientific requirement that all observations will conform to expectations. On the contrary, this is why experiments are performed over and over again. Laws (and expectations!) sometimes don’t apply or are incomplete and must be amended.