What does it mean to "honor" your father and mother?
In today's world, there are many children who have been abused and neglected. When they hear this law, they ask God "why should I?", thinking that they are to condone and support what their parents did to them, without any validation of the pain they have been through because of it.
But, while this passage refers to obedience, it is also way deeper than that.
You should treat your parents in a way that is Godly and "upright". That is honor. Regardless of what your parents do to you, you should always be the loving and kind child of God that you are. Your parents didn't choose you.
He put you where you most needed to be in order to learn what HE wanted you to learn. He put you where you are so that you can best SERVE HIM with what your environment has taught you to be.
Honor God, your Father in Heaven, first. Learn to forgive, to pray for forgiveness, and to do right in spite of it all. Remember that Jesus suffered greatly, and He endured. And, He asks us to follow Him.
Here is a great article on how to Honor your parents: