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Is the physics mainstream prejudiced against common sense?
First of all, what is clearly nonsense would be a conspiracy theory about that.  Some evil wrongdoers conspire to transform a modern, enlightened society of people who rely on their common sense if their leaders talk nonsense, back into some quasi-religious society, where Scientist are like Holy Priests, and can tell the sheeple arbitrary nonsense because this is Scientific Truth.  A prerequisite for this endeavor would be that the people give up their common sense if they evaluate scientific claims.  So, they decide to start to corrupt scientists, at first the physicists, because they study the foundations, and once the foundations are no longer something one can understand with common sense, but unthinkable mystics, everything is fine, the sheeple will be taught that understanding modern science is impossible, and they will accept nonsense about economy, climate and so on too.  A nice idea for a dystopian sci-fi, but I'm sure it has nothing to do with reality. 

But it does not follow that there is no prejudice against common sense.  I think there are two reasons for this:

1.)  The zeitgeist, the spirit of the time when the great relativistic and quantum revolution has happened.  This was certainly not a time when common sense was in high value. In politics, old values of the society have been rejected, monarchies destroyed, new communist and fascist societies, which more or less completely rejected old society, have been created.  Women's liberation and gay liberation started. In art, impressionism, cubism completely rejected common sense about what is good painting.  In mathematics we had also a revolution in the very foundations, logic and set theory.  And in philosophy, we had logical positivism.  So, everything around was a revolution against what was the common sense of the past.  Scientists are human beings, thus, one should not expect that the zeitgeist does not influence them. I think this plays a role if one wants to understand why revolutionary, positivist interpretations were favored against common sense compatible interpretations.  

2.)  Modern physics education selects those fascinated by mystics. Physicists, one can plausibly assume, are people who were fascinated by physics in their childhood and youth.  But physics, at the level one can access at the school, at least if one is interested, already contains the basics of relativity, with Einstein's trains and so on.  The way this is presented in no way suggests that common sense will be a reliable guide in physics.  And modern popular presentations of gravity by Hawking or string theory present the universe as something completely mystical, impossible to understand with common sense.  It is very reasonable to assume that physics will be more attractive to those with a mystical vein.  Instead, for those who defy mystics and prefer common sense,  other natural sciences will look preferable. Such a selection bias is, clearly, also a bias against common sense. 

So, no conspiracy is necessary to explain some prejudice of modern physics against common sense.
How can common sence be determined?
Can you accept or reject a hypothesis on the basis that your authority is common sence.
So I have a view and outline it to my audience and suggest I am correct because common sence says so.
I can not understand how your view is objective.
I do not think common sense should be used as an authority.

If I would define it, I would insist that it has to be common - shared by everybody, in particular by children (which are yet less influenced by their culture) of all cultures. In particular, the important parts of the scientific method are common sense, because they are, and have to be, used by children to learn. There is plausible reasoning - what is not strong logical derivation, because strong logical derivation is almost inapplicable in everyday life. Bayesian probability theorists have shown that the logic of plausible reasoning follow Bayesian rules (Jaynes - Probability Theory: The Logic of Science, highly recommended reading). So, these parts of common sense can be justified independently, by scientific methodology, logic and probability theory, if one wants to use them.

Then, there are some basic ideas about space, time and reality, like that there is a now, different from past and future, that this now is defined objectively, that there is some observer-independent reality, basic concepts about causality - things which are rejected by the spacetime interpretation and some quantum philosophy. The question that these concepts are common sense is, in this case, not questioned. Simply the proponents of these modern interpretations say that common sense is in this case wrong. To use these ideas as an authority because they are common sense is, in this case, impossible anyway - these scientists do not accept such an authority.

What should be excluded from common sense are particular theories shared by the people in particular cultures or particular times - such theories may be common in that culture or that time, but not common to mankind. I think, this is sufficient to exclude all the negative examples used by some people to discredit common sense - like that it means believing in a flat Earth, ghosts, witches and so on.
I certainly like the idea of common sence but when I try to define it I find that I can not.
I read as much as I can about science, cosmology and astronomy and there are matters that I think do not meet my "common sence". For example in GR gravity is not dealt with as a force, upon my humble understanding, and this seems to go against my common sence and yet GR presents as a well tested scientific model which has made predictions that have been verified. Should I listen to my common sence and say there must be a force of gravity which would suggest that I can not embrace the well accepted model. I expect that many lay persons may well find the absence of a force of gravity would go against their common sence, well for the purpose of discussion lets say we have a majority to fit the term common, and yet GR would remain the current model.
Consider religion how could we refute or accept religious views on the basis of common sence.
I am not trying to be difficult and hope you can calm my concerns.
Maybe other members can weigh in with their views or perhaps a guest may comment as they pass by, even if they need to register I certainly think the OP is a matter most interesting and no doubt others will share my interest and given the aspect of commonality is a feature of common sence if it is to present as I believe you suggest then the more contributors the better we will be, or so I do hope.
First, you can, of course, prefer my ether theory of gravity, or, more close to GR, the ether interpretation of the Einstein equations of GR, instead of following GR. I would like this, of course.  Wink   In these ether proposals, gravity can be described as a force.  Ok, not such a simple force as in Newtonian gravity, but some force, which also depends on the velocity of the body.  

The alternative would be to better understand the mainstream point of view.  But let's look at the equation of motion of a point particle:

\[ a^\mu = \frac{d^2x^\mu}{dt^2} = \Gamma^\mu_{\nu\kappa} \frac{dx^\nu}{dt}\frac{dx^\kappa}{dt} = F^\mu/m. \]

This is this relativistic four-dimensional denotation,  and it also contains terms similar to a classical force.  But what is the point of naming something a force?  It is that if there is no gravity, there is no force.  And in this case, the particle follows a straight line.  And, even if there is gravity, the force is what makes the difference between the straight line and the trajectory.  

In my ether theory, as well as in the ether interpretation, such a notion of a "straight line" exists.  It exists, it is defined by the equations, but it is not easy to measure.  In fact, there is no simple, local possibility to measure it at all even in my ether theory.   And in GR, the situation is even worse - there is not even an equation for what would be the straight line to compare with. 

On the other hand, I would not name the idea that gravity is a force "common sense".  This is already a quite special theory, namely Newtonian mechanics, which defines what forces are and how they influence how things move.

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