My theory is that people are intrinsically repulsed by things that lack order, are asymmetrical or stand out in general. If you are ugly the proportions of your face are somehow contorted: big nose, uneven eyes, recessed chin, lacking jawline etc. Are all deviations from the standard model of the human face.
this repulsion has to do with the fact that everything that is ordered in the universe tends to thrive, including the human genome for which a perfect stability is paramount to everything else.genetic mutations are equivalent to deviations in genetics, if you want examples of what kind of an effect mutations have you can look at ppl born in Hiroshima and Nagasaki, some genetic changes can be positive but they are usually minor ones. Ugliness has to do with the assumption that the deviations in your face are representative of the structure of your genes.