The problem is that in the social 'sciences', this is often treated as a 'everybody is right' instead of the approach of the physical sciences: "I'm right, and if you don't believe me, go do the experiment yourself".
That's a monumental difference that a lot of people just fail to grasp, even in serious fields of study. Just read this essay [columbia.edu] by Richard Feynman where he explains what it means to be properly scientific.
Nonetheless, students questioning their professors is not seen as a problem even in the physical sciences. For example, I had a very vocal disagreement with one of my Physics professors once. I simply refused to believe that what he was saying was possible. He was so impressed that he offered me a research position based on that one interaction.
Of course, this comes with a huge caveat -- I didn't 'just' disagree.
What had happened was that we were studying solid-state lasers, like the type you get in your DVD player or a laser pointer. They are made from crystals of semiconductors, like silicon, germanium, arsenic, etc... He was specifically discussing silicon lasers emitting light at about 650nm. I sat straight up and thought that's crazy -- I've held pure silicon in my hand before, and it looks like metal. Sure, it's a bit dark, but I just couldn't imagine how light that's "just barely infra-red" could go straight through the thing with nearly 0% loss, which is what a laser requires to operate. I argued with him -- surely it's very heavily doped and it's actually a compound of silicon that transmits the light? No. Maybe it's just a very thin surface layer, like transparent gold leaf? No.
The day after that, I was in the lab, and there was a piece of silicon there -- scrap from the chip lab. I took an incandescent lamp that I knew put out most of it's heat energy in the right infra-red range, put my hand in front of it, and then I waved the silicon wafer back and forth between my hand and the light. It's like it wasn't even there -- it blocked none of the IR light. There was no visible light going through, but I could feel the heat on my hand. I compared it to glass and various thicknesses of paper and plastic sheets. Only silicon transmitted all of the IR heat energy. It was like it was made of smoke. Sure, it was a primitive experiment, but very convincing in a I-can-feel-it-with-my-own-hands kind of way.
The next day, we were back in the lecture hall, continuing the topic of silicon lasers, and the lecturer jokingly asked me if I still had problems believing that silicon was transparent to infra-red light. I said no, I tried passing IR light through a piece of silicon in the lab. It doesn't look like it should, but it does.
That change in my position is the very essence of science -- not that disagreeing is bad, but there ought to be a method by which we can all become convinced of the truth and agree on it.
Sadly, the scientific method is not followed rigorously in many fields. Psychology and some areas of medicine come to mind. Just read: Why Most Published Research Findings Are False [plosmedicine.org] for an idea of just how far it's possible to stray from the truth because of only small errors in the application of the scientific method.
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