Well, at least we’re not in the middle ages, when every conceivable atrocity against groups and individuals was justified by the fact that they were different in some way. It’s better now, at least in some parts of the world, than it was then. Of course, there is still a good bit of hate and cruelty, and we usually just bemoan it as a part of human nature. It isn't.
People have very high standards for themselves. As psychologists point out, we don’t like to see ourselves as not meeting our own expectations. People naturally try as hard as they are able to meet their own goals, so "trying harder" is not a solution. People certainly don’t want to lower their expectations either, so they adjust their image of themselves instead. This temporarily solves the crisis; our expectations are intact and we don’t have to try and improve our behavior and performance to a level above what is possible for us.
Unfortunately, this image shift has some rather undesirable side-effects. Whenever we have thoughts or feelings that do not fit in with our superior self image, when we are ashamed of our thoughts, we shove those thoughts and feelings out of our conscious attention. We are afraid of such thoughts; they threaten our self-image at a fundamental level.
These thoughts do not go away; they are still in our minds. Thoughts have their own energy whether we are paying attention to them or not. Similar thoughts attract one another and form structures. People who are involved in creative mental tasks experienced this constantly. When they work with related thoughts and ideas, these thoughts begin to form themselves into hierarchies and patterns. Thoughts that we fear are no different; they create mental landscapes of what we fear the most within our own minds.
When something reminds us of these fearful thought structures, we experience a sudden surge of hatred, fear, or disgust as our conscious attention is momentarily focused on our unacceptable thoughts. Because we cannot accept these thoughts as part of ourselves, we assume that the feelings they generate are coming from whatever or whoever reminded us of them. This is called projection. Anyone that seems vaguely menacing can cause us to project our own suppressed anger onto them. This anger seems to be separate from "our own" thoughts, making it easy to believe that the anger is coming from the other person. Someone with different customs can prompt us to project any anti-social or simply unconventional thoughts of our own that disturbed or disgusted us, making the person before us seems disturbing or dangerous. Depending on the force of our suppressed feelings, people who are in fact harmless can appear to be capable of bringing down civilization.
Well, that was a long exposition, but it boils down to this. The more you accept your own thoughts as normal and natural, whether they offend your sense of decency or not, the more clearly you will be able to see the world