There are many people who find it difficult to wrap their heads around the hatred that displayed toward theists by atheists such as Christopher Hitchens, P.Z. Meyers, and Richard Dawkins. Many write it off as simply hatred against those in disagreement, others claim the hatred is simply doubt about atheism being manifested as anger toward Theism. While there is a bit of truth in these explanations, they do not explain the anger for one basic reason. They dramatically under estimates the effects of believing something is really true, especially when that something concerns the existence of God and moral standards.

Most, if not all, atheists have bought into the theory of evolution, which makes very clear statements about good and evil, the nature of man, and what the world should be like, or what utopia should look light. In general, good is strong, pleasant, and natural, evil is weakness, pain, and self denial. Man is only one step on the evolutionary ladder and is not intrinsically more valluable than any other organism, and the world only progresses as fast as evolution. These statemnts are in direct contradiction to the tenents held by many theistic belief systems: God determines right and wrong (our enjoyment has little or nothing to do with it in the short run), man is unique and above all animals, and history will end with mankind going to heaven and hell.

Now, if everyone were to stay at home and hold these beliefs to themselves, there would not be as many arguments. The problems arise when we try to make laws, run nations, and set policies. If you oppose abbortion, stem cell research, or euthanasia, then you are obstructing the atheistic march to utopia by slowing evolutionary development in the human race. If yuo oppose gay marriage, incest, bestiality, or polygamy, then you are opposing good (pleasure, that which is 'natural') and advancing evil (denial of one's urges). When you support prayer in school, the mention of God in the pledge of allegiance, or the mention of Intelligent Design in schools, you are filling children's heads with nonsense from humanities dark and barbaric past, ideas scientific atheism hates as much as most people hate Fascism (which is, by the way, good atheism).

Thus, Atheists have no problem with theists who leave their beliefs at home, but their wrath is hurled up at those theists who point out the harm in atheistic ideals and attempt to prevent them from implementation. Another way of looking at it is a comparison of war. In wars such as the American Civil War, the Napoleonic Wars, there was a measure of respect between soldiers. Religious war is different, combatants in a religious war are fighting because the other side is evil. Thus, there is no respect between sides. Theism vs. Atheism is by definition a religious war. Atheists see Theists as full of ideas harmful to the human race, and thus see them as unworthy of common rules of decency and argumentative etiquette.

A brief disclaimer: Much of the above is generalization and I realize that. If I wanted to speak specifically to every case I would have to write a book. Someday I might, but please realize that there are exceptions to just about everything I said, but the general rules still holds.

A Case of Mistaken Identity

If you listen to most scientists, the war between Science and Religion has been long and bitter, though Science seems to be gaining the upper hand. Even many christians speak of the war between Science and Religion and its effect upon our lives. As Judge Benton Eskew once told me, 'I can win any argument if you let me define the terms'. In talking about Science vs. Religion we have allowed Humanists to define the terms. We can argue all day whether science and Religion are opposed (they are not), but the war between Science and Religion should be called the war between Humanism and Theism.
When an atheist speak of Science vs. Religion, what he is saying and what people are hearing is 'Rational Analysis' vs. 'Irrational Faith'. That's kind of like labeling the sides in a criminal trial the Guilty and the Innocent, you cede the debate before you begin.
Evolution did not arise from someone looking at the evidence and saying 'Wow, this must have come about by chance'. Evolution arrose when Darwin attempted to explain everything without god....which is the first point in The Humanist Manifesto III:

Knowledge of the world is derived by observation, experimentation, and rational analysis. Humanists find that science is the best method for determining this knowledge as well as for solving problems and developing beneficial technologies. We also recognize the value of new departures in thought, the arts, and inner experience—each subject to analysis by critical intelligence.

Evolution and naturalism are subsets of Humanism, just as Creation and Supernaturalism are subsets of Christianity.
Humanism is not somehow more rational, more tolerant, more helpful than Theism. It begins with the assumption that there is nothing in the world besides matter and then proceeds to prove that by using purely material proofs. It is like the man who steps into the room and proclaims “There is nothing in here that I cannot see!” and then proceeds to prove it by looking around the room.
If Christians want to have a prayer of winning the war between Theism and Humanism, we must define the terms correctly or we risk being counted out before we get into the ring.