We all know the popular brand of atheism which tends to poke fun at religion and assert its truth by appealing to science and rationality, right?
I've come to see this type of atheism as reactive rather than proactive, and makes people seem arrogant rather than pushing them to understand the deeper issues.
This reactionary atheism also makes religious people angry rather than logically convincing them of anything. I don't think logic and rationality are the best tools in these types of arguments and this is why:
Contemporary religion and the increasing level fundamentalism is a reaction against techno-capitalist culture where everything is ultra rationalized to the point where some people are not feeling satisfied or fulfilled in an environment they perceive as sterile. Most atheists think more rationality and logic is the cure, but this is a mistake since its like adding fuel to the fire; they will only get firmer in their beliefs since someone is trying to give them more of the "problem".
Look at it this way: If a religious person tries to convince you that they are right, they will give you mystical reasons which, in your perspective, is just more of the problem. As an atheist, one should consider arguing in ways which do more than just shake up the hornet-nest.
Appealing to the motivations of the other person is one of the most effective ways to argue. If their problem is a lack of emotional depth in the world, than maybe atheists should consider their sense of reality rather than appealing directly to science and rationality. This is not to oppose emotion to science, Carl Sagan does a wonderful job at articulating the two simultaneously.
I don't condone the religious atrocities, nor do I have anything against science and rationality. Although I think the popular brand of militant atheism is probably liberating for people who have recently 'came out', I encourage people to develop more sophisticated ways of looking at the issues rather than getting stuck in a reactionary rut.