In order to write the truth within the world we have created, as writers we must understand each and every one of our characters, and love them. We need to know what makes them tick and why they do the things they do. Not only will understanding all of your characters help you to love them, but it will also add a new depth to your story. And this includes those nasty villains.
Think of your favorite book. Now think of the antagonist. Was the antagonist entirely evil for no reason. Chances are he or she had a past that hurt them, creating this new direction in life that made him or her the antagonist of this story. The author probably understood this concept of loving and understanding all of the characters they wrote, adding that extra depth.
Think of it this way. No doubt you've been hurt at some point by someone else. I'm going to bet that the person who hurt you was not out to hurt you, or evil. On the same note, you have probably hurt someone else at another time, and you're not evil. Everyone has reasons for their actions. Most of all, no one thinks of themselves as bad or evil or wrong, or the antagonist of any story.
Therefore, we need to truly understand our characters. And in understanding them we learn to love them. We need to get inside them and figure out what it is that makes our antagonist the "bad guy." Give them pasts, weaknesses, and pains they must bear. Possibly it is through this pain that he or she has become that person who is antagonizing the heck out of your wonderful protagonist's journey.
Put yourself in the shoes of your antagonist and ask yourself these simple questions. If I were this antagonist what would I do? Why?
As Robert McKee says in his book, Story:
"If you can't love them, don't write them."