It is the devoted single-mindedness to the notion that faith and 'god-belief' are the root of our problems that I find disturbing. The twin altars of science and reason have become an 'establishment' in their own right, claiming to have - or rather to be - the solution to these problems.
The root of the problem is tyranny, and both religion and government are guilty of it. Religion and violence are actually very similar in the respect that they both put a stop to reason. When I get tired of debating you and punch you in the face, I have declared that I am right and you are wrong- end of discussion. The same goes when someone gets their morality out of a book. If you're not using your reasoning abilities to their fullest extent, then you are more inclined to make poor decisions, potentially very harmful decisions, and that is the inherent evil. Any belief based on faith is a rejection of reason.
Science and reason are absolutely worthy of being pursued as solutions to problems. No one has a monopoly on them. There is certainly poor science and poor reason, and those are often propped up by establishments, but that doesn't mean we should stop exploring, experimenting, putting our heads together, and trying to learn more about the world around us and our social interactions in order to solve problems. Good science and good reason acknowledge that they are not perfect and there is always more to learn.
I respect a person's RIGHT to believe in anything and to promote that belief without force. That does not mean I respect the belief itself. I consider certain beliefs to be irrational and therefore evil to some extent depending on how much it distorts one's ability to reason. I am much less inclined to argue with a religious person when they respect my rights because they seem a lot more reasonable than your typical evangelical. However, I do reserve the right to attempt to persuade. To give an example, I know of an anarchist and Christian who believes in living for others and that if he does so, God is going to look out for him. So he doesn't put much effort into preparing for a rainy day, or even many days.

But magical things aren't going to happen to solve his problems. This person's irrational beliefs are very possibly going to cause harm to him and those who care about him. I've been reluctant to debate his religious beliefs because he doesn't push them on me, but now I find myself reconsidering.
And just because secular humanism is bad doesn't mean religion is good. The government attacks religion because it's a challenge to its power, but that's because organized religion is a power in it's own right. The government sides with the weaker religions right now because it undermines the more powerful ones, just as it once sided with Saddam and Bin Laden. It was expediant at the time. Organized religion, like government, has caused tremendous harm throughout history. You can't say religion must be right because it challenges the power of government. That's like saying America was right to invade Iraq because Saddam was a tyrant. No, two power-abusers were just struggling for authority.
People need to accept that others don't share their beliefs and even think those beliefs are irrational and are sometimes going to take advantage of their freedom of speech to say so. We have good reason for choosing to take advantage of that right sometimes. Make your case against such statements instead of emotional reactions
and ad hominem attacks.
To be fair, I've also seen over-reactions from the other side as well when their beliefs are challenged, like in the Christian Anarchy thread. Yes, there are also obnoxiously evangelical atheists.

EDIT: Removed the "ad hominem attacks". On 2nd thought, that was over-reaching. Being generally dismissive is more like it.