It should surprise no one to hear that there is a difference between violence done in the name of a religion and violence done because of a religion. Human beings are a naturally violent species. We fight over wealth, resources and territory. We seek to gain some form of power over our fellow men, and of course prevent them from gaining that power over us. Essentially, the common denominator in violence is not God, but man.
Sometimes, religion is used to justify violence. Democrats, for example, can often be seen justifying abortion by attempting to pass it off as just the Christian thing to do. Already most unbelievers will hopefully see the problem. I could have just chosen a random example of a "Holy" war and shown why Christianity does not support it. Instead, I flipped the objection, condemning an act of violence that is never used as an argument against Christianity. No one says "Christianity teaches that abortion should be legal, therefore Christianity is evil." Why? Because although there are some so-called Christians trying to support abortion with Christianity, everyone with any kind of education knows Christianity is diametrically opposed to the wholesale slaughter of innocent children.
So why should other forms of violence be any different? Holy war, forced conversions, cult sacrifices, anything that typically falls under the category of "Christian violence" (which hilariously involves Anders Breivik, an opponent of Christianity who claimed to be an Odinist) can be dismissed by the simple fact that even if they are done in the name of Christianity, this does not mean they are even remotely connected to Christianity.
The wonderful thing about Christianity is that whereas atheism has no official rule book that would prevent one claiming Josef Stalin, for example, was acting consistently with his atheism, Christianity has this helpful little book known commonly as "The Bible", which thoroughly describes everything one needs to know about Christianity (2 Timothy 3:16-17).
The Bible is morally opposed to most forms of violence. There are, of course, exceptions. I can already hear the tapping of keys as an angry atheist brings up the many examples of violence in the Old Testament, particularly the military conquest of Canaan and the (now obsolete, thanks to the crucifixion) commands for capital punishment for certain sins. But an in-context reading of the Bible shows that the default attitude a Christian should have to violence is to not rush to it. Most notably, in Romans 12:18, we are told "if possible, so far as it depends on you, live peacefully with all." In other words, if violence is avoidable, avoid it. Using just this one verse, you can immediately condemn every example of when a Christian has resorted to violence that wasn't absolutely essential.
Who among you would condemn acts of self defence? If someone swings a knife at your wife, you're not required to sit there and watch as he spills her blood, you have every right to fight that person, and no sane person would deny you that right. Neither, then, does God. Similarly, when Hitler was gassing Jews and expanding his territory with tanks, bombs, and guns, it was entirely legitimate for countries to unite to stop him. But what does Jesus say to do with people who reject the Gospel?
In Matthew 10:14, Mark 6:11 and Luke 9:5, we see our answer. Jesus commanded His disciples that whenever someone rejected their message, they were supposed to pull out an AK-47 and mow down every living thing within a 10 mile radius. I am, of course, being sarcastic. The actual command was to leave, kicking the dust from your feet as a testimony against them. In Acts 13:42-51, we see a live example. The disciples preached in Antioch, the Jews rejected them, so the disciples constructed several bombs and blew up city hall. Again, sarcasm, they actually kicked the dust from their feet and moved on to another city, just as Jesus commanded.
It is significant that there are zero acts of violence committed by the Apostles in their witnessing strategy. They did not stab, hang, or burn a single person in an attempt to spread the faith. They, like their God, were peaceful, calling people to repent but speaking only of a future judgement committed by God Himself for those who refused.
Now, if we're supposed to remain completely peaceful until God Himself comes back to judge the world, there are only two alternatives for a logical atheist to consider. Either Christianity is false, and thus it will always be a peaceful religion because God is never coming back to judge the world, or Christianity is true, and thus any "Christian" committing violence in Jesus' name may, themselves, be cast into Hell (Matthew 7:21-23).
In both scenarios, there is no precedent for Jihad in Christianity. In the former scenario, atheists shouldn't need to paint Christianity as violent, because there should be more factual ways to refute it. In the latter scenario, atheists really need to stop trying to make Christianity out to be violent in order to prove it wrong, because the judgement is coming, and you really don't want to be on the wrong side of it when it does. Repent and be saved. No Christian has the right to force you to repent, but God does have the right to condemn you if you do not.