When you get down to it, it's just, unfourtunately, human instinct. People react to things they don't understand with hate and fear as a survival tactic. And though you can explain things to people so they can try to understand, not everyone wants to. And even if they do, it might give them more reasons to hate and fear, rather than to accept.
As an example, lets use the Holocaust. Generally, we're told that the Holocaust was a negative thing, through cultural references and such, even if you know literally nothing about it. Then you get to history class, or you have a history-buff friend who explains it to you, and you understand it. Doesn't mean that you've sided with the Nazis though.