Then you haven't taken quantum mechanics. Anyone who says it's intutitive is lying and doesn't actually get any of it.
Neils Bohr said the same thing; but recall he was born bred and steeped in classical training; and also that in his day not even the full components of the atom had been sorted out into their proper sizes and mutual relations (plum pudding, anyone?)
In fact, from some of the comments below, a goodly number of the giants *needed* to have someone clamber up and stand on their shoulders:
SCIENCE HOBBYIST: The End of Science
Some thoughts...
Perhaps most people believe it simply because it is what they are told. I don't think religion is intuitive necessarily but has to be learnt. But the difference is, religion came from someone's intuition originally and was then told, and perhaps fits into the mold of all people's intuition because that is where it came from originally, and science came from the use of an objective methodology. Science has a life of its own, its own intuition. And so we believe now what is told by something that is not human. There is a process we follow, and this process gives us supposed truth. And when you hear about the process, it seems intuitive. Use evidence based methodologies to form conclusions. And the way we express the truth of science is in a form which is intuitive.
Idk
Glad to see the IDK at the end. I think your contention is a mixture of conjecture, misunderstanding, and perhaps some mis-classification.
Recall the Cargo Cults spoken of by the late Richard Feynman; and his discussion of psychology...not to mention medicine.
The Cargo Cults saw the planes and landing towers built by Americans in World War 2; they inferred, correctly, by direct observation that the construction of the towers, and the headgear worn by the inhabitants, were correlated with the arrival of the planes bearing hitherto-unseen goods.
So they did their best *imitation* of the towers and radios, but they didn't work; not knowing the underlying mechanism.
Similarly, Feynman spoke slightingly of psychology (hat tip to [MENTION=3325]Mole[/MENTION] for his oft-repeated depredations of MBTI *on a typology forum*

) -- when as a newly bereaved husband (to Tuberculosis, yet, so much for science being all-puissant, even for the best and brightest!), he told a psychologist he spoke to his dead wife:
Q. "And what do you say to her?"
A. "I tell her I love her, if that's all right with you!"
Q. (makes notes: third-person auditory hallucinations *confirmed*)
So psychology has the *trappings* of science, but was not able to capture the real experience of being human.
(Even with neuroscience, the mind remains synergistic; and being able to selectively interfere with one function or another cannot recreate a human from scratch.)
And medicine: even dating from the Enlightenment, a reverence for the authority of the past limited advances.
Longer ago, the sacred name of Galen halted inquiry; Semmelweis, after effectively stopping puerperal fever, was condemned to an asylum -- according to Discovery.org, drawing from the US CDC website, he died from an infection he had contracted during an operation; according to Wikipedia, he was beaten and may have suffered gangrene from it; but in any case, his opposition came from practitioners of, *ahem*, science.
Science isn't the only thing which came from objective methodology; engineering and technology did too.
Recall the ancient Greeks: the Golden Ratio, Pythagoras' theorem, ...and Zeno's Paradox. They had objective methodology and reasoning. Contrast that to the Romans, who weren't big on theory, but were great *practical* engineers. As humorist P.J. O'Rourke put it:
The Romans made a better road than anyone ever has since. For a primary road like the Sarn Helen they dug parallel ditches more then eighty feet apart and excavated the soil between them Then they laid in a sand-and-quarry-stone foundation bound on either side by tightly fitted curbs of dressed and wedged stone blocks. On top of this foundation they built an embankment four or five feet high and fifty feet wide, constructed of layers of rammed chalk and flint and finished with a screened-gravel crown two feet thick.
Even so, 1,573 years of neglect have taken their toll. The road has worn down and topsoil has accumulated along it, and the Sarn Helen has turned from an embankment into a ditch. There are washouts and mudholes and boulders in the ditch, too. But the Sarn Helen *is* still there. I doubt we'll be able to say the same about I-95 in the year 3556.
Or, one may consider refinements from the Middle Ages including the Horse Collar and Flying Buttresses: both performed without CAD software or measurement of force vectors.
So advances can and do come without a firm underlying theoretical framework.
And it is possible to have both accurate, and inaccurate intuition; evidence-based methods alone can take you a long way, but they are not sufficient.
Religion projects our natural father into a supernatural loving father called God. This is entirely intuitive.
Science takes us into areas totally outside the experience of our family in the ultra large in Relativity and the ultra small in Quantum Mechanics. Both are counter-intuitive.
What is extraordinary is that it is only in the last few hundred years that some of us have learnt to think counter-intuitively. Why is that?
Not sure that I agree with you about religion being a projection of our natural father: the cultural remnants of Christianity in the modern West give that impression: but the pantheon of classical gods were much more concerned with petty squabbles among themselves, if mythology portrays the beliefs about them accurately.
Buddhism and Hinduism don't seem to have much in the way of a loving Father: and other older religions in both the Old and New world practiced human sacrifice.
As to why some people have learned to think counter-intuitively, I think the answer to that is a combination of several items: increasing technology, in conjunction with greater health (fewer literal plagues due to improved sanitation, Athens was subject to pestilence as much as London) and more food (thanks, Medieval Warm Period!) led to the opportunity for people to do more than live hand-to-mouth intellectually, so to speak.
This was combined with the emergence of a mercantile class, for whom improvements in everything from navigation to transport, led to a great increase in technology, for the direct purposes of acquiring wealth (not to mention that somewhat of Western Civilization had to be built up to the point that there were city-states which were not being attacked constantly, and it was safe to travel from place to place -- The Pax Romana had more benefits than people realized);
the "why" of the ancients (looking for idealized causes, purposes, teleological reasons) became replaced by the "why" of the tinkerer, and thence to the "how" of the engineer; when this was combined with both empiricism *and* the inclusion of mathematical modeling, things really took off.