VJack of Atheist Revolution posts that he likes to publish stories of crimes committed by Christians to show what hypocrites they are:

The meaning of the “know them by their deeds” phrase comes from the Christian bible. Matthew 7:16 reads, “Ye shall know them by their fruits,” and translators of the Greek and Hebrew generally interpret “fruit” as “deed,” “act,” or “work.” The meaning is that it is often misleading to base one’s impression of someone on their words and that we are better off focusing on their acts. That is, know them not so much by what they say but what they do.
I use this phrase to highlight Christian hypocrisy. We all know that believers are fond of claiming moral superiority over nonbelievers. And yet, their deeds often suggest otherwise.

Unfortunately, he does what many have a tendency to do, he pulled the verse out of context. Are the “them” in this passage Christians? No, if you look at the verse in context, you see that “them” refers to false prophets:

Matthew 7:15 “Beware of false prophets, who come to you in sheep’s clothing but inwardly are ravenous wolves. 16 You will recognize them by their fruits. Are grapes gathered from thornbushes, or figs from thistles? 17 So, every healthy tree bears good fruit, but the diseased tree bears bad fruit. 18 A healthy tree cannot bear bad fruit, nor can a diseased tree bear good fruit. 19 Every tree that does not bear good fruit is cut down and thrown into the fire. 20 Thus you will recognize them by their fruits.”

Jesus is warning his disciples (Christians) against the false teachings of those who look like them but aren’t. Leaving aside the misuse of this passage, the atheist does have a good point. Why don’t our deeds match our words? Why do we act like we are morally superior when we aren’t?
These are good questions and ones that Christians have struggled with for centuries. Why do any of us do the things we know we shouldn’t? Why do we want what is forbidden? Adam and Eve were the first to discover this aspect of our human nature 🙂
Christianity is a belief that man has fallen into sin and needs a way out of it, the only way is Jesus Christ who died on the cross for our sins and was raised from the dead so that we may walk in newness of life. What the world doesn’t get is that though we’ve been given the ability to walk in newness of life, we don’t usually do it. We struggle with our sin and we can’t quite get rid of it. So, to the world we are these sinners who don’t live up to our words but to God we are sinless because he looks at us through the righteous of Christ. Luther called us snow covered dung heaps.

Colossians 3:1 If then you have been raised with Christ, seek the things that are above, where Christ is, seated at the right hand of God. 2 Set your minds on things that are above, not on things that are on earth. 3 For you have died, and your life is hidden with Christ in God. 4 When Christ who is your life appears, then you also will appear with him in glory.

Who we are is hidden and we will not be revealed until Christ is revealed. So, we know what we are to do as the Paul continues to write to the Colossians:

Colossians 3:5 Put to death therefore what is earthly in you: sexual immorality, impurity, passion, evil desire, and covetousness, which is idolatry. 6 On account of these the wrath of God is coming. 7 In these you too once walked, when you were living in them. 8 But now you must put them all away: anger, wrath, malice, slander, and obscene talk from your mouth. 9 Do not lie to one another, seeing that you have put off the old self with its practices 10 and have put on the new self, which is being renewed in knowledge after the image of its creator.

But we struggle in doing it.
When the atheists point out the hypocrisy of the Christians who commit crimes, I read the stories in despair that we prove to be such bad witnesses to the world. We love a God who is just and holy and yet we can’t reflect that wonderful nature to the world. It’s frustrating that God’s name is tied together with the heinous actions of men and women who may or may not be his. But we understand the nature of man and what a struggle it is to do the things we are commanded to do and we’re thankful that God’s judgment for the sins of Christians has been met in Christ on the cross. We understand that we do the things that we don’t want to do and don’t do the things that we should. That knowledge doesn’t absolve us of our responsibility to follow God’s commandments but it helps us to understand why we fall short of the glory of GOD. We don’t accept the actions of those Christians who are committing heinous sins but it helps us to understand why they do it.
Any Christian who believes that in themselves they are morally superior to the atheist doesn’t really understand the gospel.