[psychoslave]

You generally don't oppose to things you can grasp to the point you could understand how it challenges other beliefs you culturally or intuitively integrated.

Evolution directly challenges the idea that humans are very special creatures in a universe where mighty mystic forces care about them a lot.

Climate changes, and the weight of human industry in it, challenges directly the life style expectations of the wealthiests.

[SkyBelow]

To some extent, physics/chemistry/etc. challenge the notion that free will exists, but that challenge is far enough removed and rarely touched upon that people who believe in free will don't feel that modern science is attacking that belief, and the scientists working on it generally see free will or any mechanisms of the brain as far too complex when they are studying things on the order for a few particles or few molecules.

Some of neurology/psychology gets a bit closer, but science of the brain doesn't have major theories that are taught on the same level nor have much impact on public policy. The closest I can think of is how much public awareness of what constitutes a mental disorder lags behind science, but that area is still constantly contested even among the researchers themselves and thus prevents a unified message being given to the public that they must then respond to (choosing to believe the science or not).