A common attitude among unbelievers is that religion is the cause of all wars. There are a great many flaws with this claim, starting with the fact that "religion" is actually a broad term, like "animal". You cannot say "animals can run up to 76mph", because while it may be true of a cheetah, it's not so true for a Galapagos tortoise. Saying "religion teaches...", "religion causes...", or anything like that, is illogical. The one and only exception is when you come up with a suitable definition for religion, and then say something like "Religion is a set of beliefs concerning the cause, nature, and purpose of the universe" (1).
So, already the claim that "religion" is the root of all evil is off to a bad start. But here's the really uncomfortable question: If religion really is the cause of all evil, what caused religion? We could approach this a number of ways. We could even point out the hilarious irony that, since some atheists define atheism as just a "lack of belief in gods", and you can't believe in gods until they've been made up, therefore atheists are the cause of religion.
But of course, no matter how you approach the issue, if you believe all religions are made up, you must ultimately believe that religion comes from man. But that means religion isn't the cause of evil. Rather, it is an effect. Where does evil come from, then? Well... man.
Coincidentally, this is what the Bible also describes. The evil we see in man made religions comes from the men who made them. The hatred, the intolerance, the greed, the violence, the hypocrisy, everything atheists blame on religion only come from religion because man first put them into religion. And that's why you have terrible atheists, too. Atheists aren't immune to the problems they blame religion for. In fact, the irony is, it is often the atheistic attempts to remove religion that perpetuates the horrors of religion. How can you blame religion for war while you're launching wars against the religious? How can you blame religion for sectarianism while segregating yourself from the religious? How can you blame religion for intolerance while you fail to tolerate the religious? It's called "hypocrisy", and you can't blame religion for that if you, who oppose religion, are that very hypocrite.
So the problem isn't religion. The problem is man. The solution? Religion. But not just any religion. Man made religions are a symptom of sin. But there is a religion given to us by the Holy God, who seeks to save us. That religion is, of course, Christianity. Atheists cannot blame Christianity for evil any more than they can blame hospitals for diseases, gyms for fat people, or soap for stench. When applied correctly, Christianity stops sin.
Of course, as Christians are still human, we are not completely free from sin. And sometimes, that does result in even very faithful Christians doing some very evil things. But the problem in that scenario is still humanity. And that's very uncomfortable. See, if religion is the problem, the atheist gets the pride of not being religious. But if it's a humanity problem, there's no one left to blame but ourselves. The religious, the irreligious, we're all sinners. We've all violated God's law. Except one man.
That man is Jesus, and though He never broke God's laws, He died as if He did. Because we did. So, when Jesus died, He took the punishment for our violations. That leaves His reward open for us to receive. Receiving that reward, namely an inheritance in God's eternal Kingdom, is very easy, yet also very difficult. It's easy because Jesus did all the work for it. It's hard because it requires humility our species finds repugnant. You can't receive eternal life while you're blaming God for your problems. But if you humble yourself, confessing Him as Lord, and believing in your heart Christ raised from the dead, you will be saved. So take your pick. Continue in the folly of throwing stones in your glass house, or become a living stone in the house of God.
References
1. Dictionary.com, Religion (link)