QM is only the most recent BIG roadblock. Most of physics is counter-intuitive. Look at how long Aristotle reigned supreme with his essentially intuitive descriptions before he was questioned. That a body in motion or at rest tends to stay in motion or at rest unless acted on by an outside force is a counter-intuitive revelation that took milenia of thought to arrive at. If you traveled the remote corners of the world asking physics-naive peoples to figure out the laws behind how things move you would never find any who could arrive at Newton's first.
The very fact that physics, or any discipline, has to be formally taught is just about a guarrantee that it's counter-intuitive. Most people can hear, understand, and accept Newton's first in a minute, which makes it seem vastly more intuitive than it is, because none of them could ever have arrived at it themselves.