Children should honour their parents; the fifth commandment says so.  Obedience is the simplest proof of honour: such action demonstrates heartfelt respect.  Paul is writing to families who claim to follow Jesus Christ: if children cannot obey their parents who they can see, they will have no desire to honour God who they cannot see.  Obedient children (providing that their obedience is willing and in response to loving encouragement) are a joy to their parents, a blessing to the church and a glory to God.  Honouring parents in that way brings the promise of blessing (Ephesians 6:2-3).
 
The key is 'willing obedience'.  Any child can be bullied or beaten into obedience but that is no example of the way our Heavenly Father relates with His children.  God is as kind as a gentle mother (Isaiah 66:13): He is as compassionate as a wise father (Psalm 103:13).  The Apostles treated the young Christians in the same way: “For you know that we dealt with each of you as a father deals with his own children, encouraging, comforting and urging you to live lives worthy of God, who calls you into his kingdom and glory." (1 Thessalonians 2:11-12)  These are our models in parenting.

Paul instructs fathers to be aware that harsh treatment of a child can produce bitter resentment which may influence their whole personality.  A discouraged child will not learn properly or relate properly with others. Their whole lifetime may be coloured by the pain of feeling worthless and useless.  So, Paul warns fathers never to treat their children in such a way that a destructive root of bitterness can grow up inside them (Hebrews 12:15).  Instead, they should have clear godly instruction, appropriate encouragement, warm forgiveness and much love ... that is the right spiritual and emotional diet for any child.  Yes, warning and rebuking are important but always to be balanced by encouragement (Titus 2:15).
 
Where harsh fathering has produced bitterness, the remedy is confession and repentance - not just to God but to the child too.  Let your children see how you are growing in the grace of repentance if you expect them to do the same.  When a family tradition has been brutal - break the habit of generations by asking God to help you show love.  Where children are displaying destructive power, are they just copying your heart?  Do you show that reverent honour of your own parents and your heavenly Father?   Where a child is out of your control, don't forget that kindness and encouragement might win them back to their Lord.  That is the longsuffering nature of our God too (2 Peter 3:9) ... and He alone has the power to help them to change.  Family life is often a mirror of your own relationship with the Lord, so before blaming the child, hear what the Lord is saying to you.