I claim that one cannot enter, for the first time, into the territory of some domains of knowledge while listening to common sense voices. Our common sense will immediately reject some facts because those facts are contrary to common sense.
You must still these instinctive reactions because common sense knows nothing about many things. The physicist must still her common sense reaction at the results of some experiments regarding the inner working of the atom.
The inner working of human nature can be as mysterious to common sense as is the inner reality of the atom.
We can see only what we are prepared to see. Common sense does not prepare us to see many things. We have to creep up on certain matters and withhold judgment until we are intellectually sophisticated enough to judge their reality.
I think the Structure of Scientific Revolutions (Kant) is an excellent treatise on what you are talking about.
He doesn't talk about common sense explicitly, but the general theme of the book is that people tend to disregard real evidence in favor of things that have come to seem 'true' to them.
I am not really sure the point of the OP, although I do agree with it.
I wonder (and wonder if other people wonder) what the obviously true thing is today that all the scientists are flat out denying. It's possible of course we have it all together, but it seems unlikely to me. It's interesting, that if history is any lesson, there is a small subset of people right now who know something is true and the scientific community is not able/ready/willing to see it.