An extremely popular argument in atheism is the God of the gaps narrative. According to the narrative, prescientific people used to attribute every event, or at least every mysterious event, to supernatural agency. Indeed, that's a primary source for religious belief in the first place. Ancient people were superstitious because they were ignorant of how nature works. So they postulated supernatural agency as a stopgap.
But due to the stately march of science, we are steadily filling in the gaps. Indeed, the very success of modern science and methodological atheism go to show that invoking supernatural agency never had any genuine explanatory power. Thanks to modern science, we can propose naturalistic alternative explanations. Indeed, religious sophisticates concede scientific explanations for most events. And even when we can't currently offer a naturalistic alternative explanation, the success of secular science creates a tremendous presumption in favor of naturalistic explanations. As Richard Feynman put it,
God was invented to explain mystery. God is always invented to explain those things that you do not understand. Now, when you finally discover how something works, you get some laws which you're taking away from God; you don't need him anymore. But you need him for the other mysteries. So therefore you leave him to create the universe because we haven't figured that out yet; you need him for understanding those things which you don't believe the laws will explain, such as consciousness, or why you only live to a certain length of time -- life and death -- stuff like that. God is always associated with those things that you do not understand. Therefore I don't think that the laws can be considered to be like God because they have been figured out. P. C. W. Davies & J. Brown, eds. Superstrings: A Theory of Everything (Cambridge, 1993), 208-209.
i) The claim is a half-truth. For instance, paganism often personifies natural forces. Likewise, paganism may treat mental illness as the result of one person hexing another.
ii) It's also true that some Biblical miracles might employ natural mechanisms. For instance, Ananias and Sapphira might have died from a brain aneurism or stroke or heart attack or pulmonary embolism. The destruction of Sodom and Gomorrah might have been a natural disaster. The Crucifixion darkness might have had a natural cause. In cases like that, we'd be dealing with a coincidence miracle: a miracle of timing rather than a miracle of nature.
iii) There are, however, many Biblical miracles that resist scientific explanation, viz. regenerating the severed ear of Malchus, replicating fish, raising Lazarus from the dead, fireproofing humans (Dan 3), contact with a skeleton reviving the dead (2 Kgs 13:21), the metamorphosis of a stick into a snake and vice versa, walking on water, virgin birth.
For instance, even if it's scientifically possible to walk on water, that wasn't scientifically feasible back in the 1C. The technology didn't exist.
iv) In many cases, the God of the gaps narrative has the situation exactly backwards. The progress of science has made these miracles even less, or ever less naturally explicable rather than more naturally explicable. Take the virgin birth. About the only thing ancient people were in a position to observe was the normal correlation between sexual intercourse and pregnancy. They had no deeper understanding of the cause and effect. By contrast, we have a detailed scientific understanding of sexual reproduction. In principle, an ancient skeptic might appeal to an unknown law to explain away the virgin birth, but we now know that's naturally impossible.
v) Apropos (iv), if the God of the gaps narrative were generally true, then we'd find secular scientists offering naturalistic explanations for Biblical miracles. There is the occasional attempt to explain a Biblical miracle scientifically, viz. the ten plagues, Star of Bethlehem, Crucifixion darkness.
However, many Biblical miracles defy naturalistic explanations. When is the last time you read a secular scientist like Carl Sagan, Isaac Asimov, Richard Dawkins, Jerry Coyne, Sean Carroll, Lawrence Krauss, Victor Stenger, Stephen Hawking, PZ Myers, Steven Weinberg, or Neil deGrasse Tyson present alternative naturalistic explanations for all the miracles of Scripture? If the God of the gaps narrative is true, then they should be able to posit natural mechanisms to account for them. But what they do instead is to deny that these event ever took place.
For instance, they don't say, "Yes, Jesus was dead for about 48 hours, but here's a natural process to explain the reversal of his condition". They don't say, "Yes, Jesus was restored to life after 48 hours, but not because God raised him from the dead. Here's how it really happened!"
What they do is not to explain the event naturalistically, but deny the reported event and propose a different event to account for the "legend", viz. the body was stolen; Jesus fainted on the cross, then revived in the tomb; the disciples went to the wrong tomb, &c.
In general, they dismiss Biblical miracles as pious fiction. Yet that's the polar opposite of their God of the gaps narrative. To be consistent with the narrative, they should grant the historicity of the Biblical events, but then explain them naturalistically. It should be a question, not regarding the occurrence of the event, but the interpretation of the event.
The upshot is that "skeptics" don't really believe the God of the gaps narrative. In practice, their response to Biblical miracles is diametrically at odds with that narrative. They don't think science has any explanatory power to account for most of these events.