Whether it's Richard Dawkins, Sam Harris, Christopher Hitchens, or Dan Barker, most prominent atheists portray themselves in a very anti-theistic manner. That is, not only do they disagree with the various claims made by theists, but they see theism itself as something dangerous and worth opposing directly. They see religion as a primary producer of evil in the world, and something that the world would obviously be better without. But, I think this view is a bit myopic. It demonstrates an obvious failure to peel back the layers and investigate the true root of the problem.
Now, let me be clear -- people do do evil things in the name of religion, and I believe that, as a global civilization, we would do better without it. But, getting rid of religion wouldn't be the panacea that many claim it to be, because religion, especially organized religion, is but a mere manifestation of the real problem. Organized religion is just a product of dogmatic, orthodox thinking, and that's the real root of most evil in this world.
Anywhere where people don't think for themselves, but instead rely on authoritarian or populist viewpoints to draw their thoughts for them, mass ignorance and injustice are likely to follow. This has been demonstrated throughout history time and time again, manifesting itself as a maxim in both secular and sectarian forms. When the Church had an authoritarian influence over much of medieval Europe, there were witch-hunts, inquisitions, crusades, serfdom, oppression, perpetual ignorance, and wide-spread superstition. The typical life was short, miserable, and terrifying. When the various totalitarian regimes asserted their authority over Germany, Italy, Japan, Russia, China, and Cambodia, among others, in the 20th Century, much the same happened. The people of those countries were extraordinary unlucky that they were under such authoritarian rule in a time when technology was available that made it relatively easy to kill and oppress millions and wage war on a grand scale.
Clearly, if we can learn anything from what happened under the rule of ardent secularists like Joseph Stalin, Mao Zedong, and Pol Pot, it's that the belief in God isn't really the problem. It goes deeper than that. It's not really the beliefs themselves that cause the danger, it's the belief that said beliefs cannot and should not be questioned. How much of a problem would the belief in witchcraft or communism be, if they could be actively questioned by individuals without fear of reprisal? The answer to that question is simple -- look at Western society today. No one is being burned at the stake; no one is promoting the collectivization of business and agriculture (at least no one that is being taken seriously). Why? Because not only do we know that witches don't pose any threat, and that communism simply doesn't work well, but we can also express those truths with no fear. It's the simple fact that we have the ability assess the evidence for ourselves and the freedom to express our honest opinion of them that protects us from the evils of dogmatism and orthodoxy.
This is not to say that we can now relax and let our guard down. On the contrary, we should certainly continue to push the limits of free expression. Freedom requires vigilance and an active participation in being free. It's not out of the question that we can sink back down to the depths of a thoughtless devotion to an idea. You must at least tread to keep afloat, having a thought of your own from time to time, but why not swim with fervency to the shore, walk out of the water, and don't look back?