There is a long list of natural phenomena that were once attributed to the gods. They now have scientific explanations:
Beliefs and theories come and go. And pointing to erroneous beliefs held by people thousands of years ago would not be relevant to beliefs held by modern people.
Further, even in scientific theories, there is a wasteland of discarded or deficient theories that were once widely held. See Superseded theories in science.
Isn’t it more likely that the remaining mysteries will also eventually have natural explanations, obviating the need to invoke the supernatural?
Maybe, maybe not. But if your claim is “science will eventually have an answer”, then that is just science of the gaps.
What if there is never a scientific answer for something? At what point will a naturalist admit there is no scientific answer?
By definition, the supernatural cannot demonstrably be shown to exist. It is not empirically observable or measurable. Again, let’s take the multiverse. It would be impossible to measure or observe it. Do scientists outright throw it out because it cannot be demonstrably shown to exist?
Let me state that I’m not advocating giving a supernatural explanation for everything we don’t have an answer for. Just because I cannot find my matching sock after I dry my clothes doesn’t mean it was stolen by something from the upside down.
What I am advocating is looking at all the evidence and if the preponderance of evidence points to something, then it is a viable explanation, even if it is supernatural explanation. This is the approach I’ve been taking all along in this thread.
And to reiterate, the scientific method does not state the supernatural does not exist. It only assumes the supernatural does not exist. Probably 99.9999% of all things can be explained naturalistically. But, not 100%. For those few cases that cannot (and most likely never will be explained) naturalistically, then the supernatural cannot be ruled out.