I believe we are shaped by our experiences over time and that those experiences cause perception to be fluid. I also believe that if we decide to change our perceptions that stem from our environmental experiences, we can work to do so. I would call what you describe as skewed perceptions either filters or lenses through which we see the world; albeit everyone's filters are different based on experience and choice.

I'll use religion as an example because you did. In my case, I was raised in a non-churchgoing home with traditional values, but all 13 years of my schooling was in a fundamentalist Christian sect. I am still affected by my experiences at that parochial school; however, I am working to change those automatic perceptions in therapy. I have had success with this.

Now think of someone who has autism; they view the world through a biologically programmed filter on top of the filters or lenses of experience. It is difficult to overcome a biological filter. People have much less choice over that.