Are stigmas and and prejudices, inherently based on fear, ignorance and hatred?

[Neo-Scholastic]

Many emotional responses are instinctive. People tend to fear snakes and spiders not puppies or ducks. People are also naturally inclined to distrust strangers. People are averse to dung and vomit but crave sweets and fatty foods. Understanding a threat does not entail ignoring its danger. The question at hand is not the origin of natural feelings or instincts but rather how to attain the judgement to know if and when we should use reason to overcome what nature imposes or to comply with it.