Mutants can also be villains. Sometimes their powers corrupt them or make them want to dominate others. For instance, in some horror - fiction mutants are created by some sort of experiment gone wrong and they terrorize normal people.
They can be heroes. In many superhero stories, mutants use their powers for good, like saving the world from villains. For example, in 'The Incredibles', the family has special abilities which could be seen as a form of mutation, and they fight against evil to protect the city.