re: OP
I agree, to some extent.
Some scientists like to Ockham's Razor anything that is not explained by the current framework of science out of existence. But the whole point of Ockham's Razor is that it is a scientific heuristic, not a test of truth.
I think that a lot of people, probably more individuals in the general public than scientists themselves (but let's be honest, a lot of scientists too), tend to confuse scientific methodology with tests of truth. The fact that a scientific theory should not assume the existence of God, or the soul, or midi-chlorians does not in and of itself invalidate the possibility of a truth involving God, or the soul, or midi-chlorians. We just don't have the tools to understand these things yet.
And to your deeper point (rather than my spin on the point it looks like you're making), I agree that at some point, we will be able to gain a more thorough understanding of things that at this point seem supernatural. At the very least, it's a possibility.
Still, I think that there is something to the claim that there are areas that science, at least presently, is unable to explain, and so must remain agnostic about rather than assuming their nonexistence:
I was reading a great article once about how a guy was walking with his kid, who explained to him that science had proved once and for all that old, silly fantasies like faries never existed. And of course, the dad retorted that science has proven no such thing. Science *can't* prove or disprove the existence of fairies, God, the soul, alternate universes, or midi-chlorians, because these things are by definition supernatural, i.e., not obeying the laws of nature. Since science must take as its starting point the laws of nature as we currently understand them, supernatural things are excluded from scientific study by definition. However, "excluded from scientific study" and "contrary to the laws of nature" are not synonymous with "non-existent," whatever David Hume's ridiculous argument against miracles would have you believe.
(Although, to your point, "supernatural" = "not obeying the laws of nature" is a bit of a misnomer. In reality, "supernatural" = "not completely explainable using the laws of nature as we currently understand them." Things are magic until they're science, and they're science until they're magic.)
And so the proper position on such subjects is at the least agnosticism. Technically speaking, if you're a pure rationalist of the gung-ho Descartes streak (i.e., you refuse to believe anything that cannot be demonstrated with certainty by reason), the proper position towards everything is agnosticism. (Descartes had to prove the existence of the physical world via a proof that essentially says that God is true by definition, and the further assumption that a perfect--and therefore, necessarily existent--God wouldn't let us be deceived like that. But if you can do better than Descartes, be my guest.)
Overall, I like David Eagleman's take on it all. I was listening to an interview where he talked about how science establishes a zone of possibility, in which certain things can be ruled out as not possible given the facts as they stand, but which leaves open a wide space of possibility, especially when it comes to the afterlife and such things. He has a cool book called Sum that I really want to read that presents like forty different possible afterlives. He's like a quintessential alpha NT kind of scientist. I'm pretty sure he's ILE.
One could use essentially the same semi-Freudian lines of reasoning that "prove" religion only existed to keep people in line, to "prove" that the only reason you hate religion is because you didn't get along with your dad or had a basic need towards individuation during adolescence. Anything can be Freudified to death, literally anything, just like any word can be read out of existence. Interpretation is a trap. When you start speculating on motive, you can reduce anything to whatever you want to reduce it to.Can't people just please read some fucking history and realize that religion is just a big black box used to explain the things we dont understand and get people to cooperate?
It's a lot smarter, I think, to take a nuanced and balanced view on things, including religion. So I think it's smart to recognize that yeah, a lot of the impetus for religion does come from a desire to explain things that, yes, science and the pseudo-science of Freud-style psychology go a long way towards explaining.
But at the same time, let's not pretend that this puts the question of religion to bed.
Even if you can prove conclusively that the only reason people have the general "love thy neighbor" sentiment is that "love thy neighbor" gives them a way to safeguard themselves from losing the object of their libido by generalizing the libido to include everyone, have you really proven that a person who genuinely loves his neighbor for no other reason than that the neighbor is a human being, is a worse person than one who is indifferent towards anyone that is not a close friend of family?
Similarly, even if you can prove conclusively that people believe in religion because they want a way to explain the unexplainable, does that really prove that religion is false, harmful, or "bad"? I don't think so.
And on a related note, the fact that religion has been used for the purposes of those in power, as noted by Machiavelli in Livy and elsewhere, does not make religion itself bad. The United States funded most of the original research that led to the electronic gadgets we use today because they thought the research in question would help us get better at killing people. Does that mean that the gadgets, or scientific research, are bad?
Also, common sense side note: EVERYTHING can be and has been used for the purposes of those in power. If anything, religion has proven pretty damn slippery for the uses of those in power, certainly more slippery, on average, than artists. Hasn't religion just as often been on the other side, against those in power? Like, I dunno, the entire history of Christianity from ~50AD when Saul was killing Christians to 313AD when Constantine flipped? You're not going to convince me that Christianity grew because of state support while Nero was having Christians burned.
Your early history loses to my early-er history. Deeper magic from before the dawn of time, yo. (Actually, the whole Christianity thing happened after the arguably mythical bits in Livy that Machiavelli was talking about. I just really wanted to make a C.S. Lewis joke.)
I've read Discourses on Livy too, and bully on Machiavelli for noticing that religion can be used for political purposes. While we're Freudifying everything, we should also mention that he had a political bone to pick with the church of Rome, and probably had some personal stake in reducing the function of religion to state support.
What I'm saying is, religion must be considered as a thing separate from any one outcome or any one possible motive, positive or negative. It's reductive, intellectually dishonest, and historically ignorant to reduce religion to either a) its negative uses by what Machiavelli might call "temporal" power, or b) the desire to explain away what we do not understand (or convince a group of people to take collective action). If nothing else, we can counter that by referencing a) the positive social actions taken by religious groups, b) the ability of religion to provide a framework for what we cannot understand (i.e., tragedy, death, etc.), and c) the MANY times in history in which religion has been the impetus for a group of people to break the status quo, like, I dunno, those people who decided to defy all the orders to stop following their religion or die, from everyone from the Emperor of Rome to the Communist Dictators of Russia. They're called martyrs, and just talk to the Catholic Church, they'll give you a list of zillions of 'em, like freakin' one for every day of the year. #highchurchjoke.
Summary: I'm not saying religion is perfect. I am saying it isn't just "a big black box." Nothing is just a big black box. (Yes, please do quote the preceding sentence and post a picture of a big black box).
Side note: just because mainstream Christianity in America has a decidedly conservative bent, doesn't mean Christianity, much less Jesus of Nazareth, had a conservative bent at all. Trust me, Jesus' message is comprehensive enough to offend left-wingers and right-wingers alike. (protip: read what he actually says about money).