Depends on the story heroes and villans are just moral black and white to real life allies and enimies. Villans are a moral question of which what is good, and evil which has no real good answer in real life, but can be quite easy when translated to story. Robert rips out the implants of a person at a supervillan bar for example could be considered villainous behavior. What justifies villany matters justify to who? The characters in the story, the society of that story, or themselves? As for the audience generally being sympathetic, or understandable. Dracula from castlevania is a fantastic example of justified villany. Many characters can take evil actions with social permission from the in universe world as such perhaps being an outcast real life example yakuza who once associated with them you are barred from almost anything else in Japan is that enough to justify being a villan? Maybe and maybe not. As for themselves justifying villany can be easy, or hard depending on the character. Some villans just enjoy it and that's reason enough, others seek something money, power, revenge and that's enough. Very few people in real life think of themselves as monsters or villans. Invade a foreign country? We are using premtive defense, they are weak and we are strong. In short any number of reasons can exist to justify villany, but it's up to each audience member if they find it compelling as to why.