I think it's just lack of basic algebra skills. If you have never been taught to think about math in an abstract way, you will naturally approach problems this way instead.
In Ancient Egypt for example when they needed to explain things like the Pythagorean theorem they would give examples, because there was no concept of abstract variables yet. I think this is similar.
In the same way, many people are comfortable working with vectors, transforming them with matrices etc but they have never been taught to think of transforms in an abstract way. So if they want to check if a certain matrix actually performs the transformation they want, they apply it to a bunch of random vectors to see if it's reasonable instead of just checking what it does to the base vectors, because they have no real concept of linear transforms, and only vague ideas about dimensionality and degrees of freedom.
To some extent it IS phobia, because if you just want to rotate a vector 90 degrees you don't really need concepts of orthonormal transformations so you might be reluctant to look at it that way, but if on the other hand abstract algebra is very natural then the abstraction is trivial to do, it just makes things easier.