Given the fact that the New Atheists are becoming more bold and violent against Christians, and the fact that Atheism has the most violent history of all religions against followers of Christ, some Christians have become fearful. This is wrong. Fear leads to anger and anger leads to hate.

1. This fear, anger, and hate does not proceed from the Holy Ghost. It is not of faith. Whatever is not of faith is sin. Sin is what takes us out of the Kingdom of God and into the kingdom of Satan to be a slave of Satan. Love is what takes us out of the Kingdom of Satan with its slavery to Satan and into the kingdom of God.  The human mind always serves either Christ or Satan, and Satan rules the human mind through lies.  It is the Truth that sets us free.  Christ is the Truth and the only Source of Truth.
2. Avoid being drawn into arguments. You will find that the problem is almost never that the Atheist is not aware of their illogical thoughts. Even if you absolutely show them that their belief system is invalid, they will not turn. You must show them Christ in your life. They must see Jesus or they will never turn to Him.
3. How can we fulfill the command of God to witness fearlessly to the Atheists unless we love them and care deeply for their souls? There may even be physical danger in doing so, but there has always been physical danger in following Jesus. We are to pour ourselves out on God's alter, and caring for Atheists to the extent that we are willing to die is part of dying to self and living to Christ.
4. Talk about your experience with Jesus, how He leads you and speaks to you and does His work through you by His power.  The scoffers will scoff and claim that you are not experiencing what you are experiencing, even though it is neurotic for them to do so.  On the other hand, thoughtful Atheists will listen and reflect.  When they hear you speaking by the Spirit, God is able to touch them.  Faith (the supernatural belief and trust of God that is a free gift) comes by hearing and hearing by an utterance from God.