Staunch advocates of militant atheism (like Richard Dawkins) often bring up how religion encourages acts of violence and is thus a threat to society that must be combated. However, there are many, many problems with this argument, and this approach to religion as a whole.
Let’s have a look at history–say, the crusades. Those were Christian kings that believed that they must take back the holy land for the purpose of [politics, money, power, religion], and a common point is that they would not have had the will or justification to be violent if they had not believed in god. Probably true. However, that was a few centuries ago. Western civilization has become more advanced, and more secular over the years, and as a result, we no longer start bloody crusades against those who do not believe the way we do. There are those who would like to (the evangelical right-wing), but they do not have as much power because we are more or less a secular society. In order for them to have less power, we must continue to separate religion and the state; doing so is the path of civilization, and will only result in our society becoming more less combative and more advanced.
Look at where the religious violence occurs today: in places that are uncivilized. The middle eastern societies are chronologically challenged in many ways, the major one being secularism. Religion rules their society like Catholicism ruled medieval Europe, and there we see a great deal of violence (just like in medieval Europe).
I do encourage the fight for secularism, but not the fight against religion. That just turns us into the same sort of intolerant pricks that we accuse them of being, and trust me: no good southern Baptist gives a rat’s ass about the logic or probability behind all of it.
Here’s the part that makes me optimistic about the whole thing, and the reason that I don’t see a need to attack viciously, like Dawkins does. The more we fight for scientific, empirical standards in schools and other places where kids go, the more it becomes likely that these children will have a chance to see the light beyond their parents’ religion. However, it is wrong to encroach on their right to believe whatever the hell they want to-giving them that right is the sacrifice we make by having a freedom of religion clause in our constitution. Most Christians or Jews or Muslims who live in western countries are not at all a danger to society-there are many great doctors, scientists, lawyers, firefighters, etc that believe in god, as you must know. The numbers of the ones that cause trouble are getting smaller and smaller, most often reduced to small country/rural areas. We are getting more civilized, and as we do, religion will become less something that people feel the need to fight and more something like left-handedness vs. right-handedness.
As for the middle east, we must simply help them along the road to secularism, although it will take a long time. In the meantime, you can expect more violence from those areas. [Digression: I wish there were a presidential candidate who would acknowledge that religion is the problem over there, but there isn't... it's hard (because we aren't secular enough yet) for someone who's simultaneously smart, logical, and honest, to be elected to public office... but we're getting there]
Also, I would make the example of Ken Miller, a Brown professor who staunchly advocates evolution and is also a Christian. The beauty of our free, civilized society is that one can hold religious beliefs and think logically and empirically at the same time. We are not sacrificing our nation’s youth to the savage jaws of a lifetime of close-mindedness. Every generation becomes more secular, and every generation has more parents that encourage their children to ask the all-important questions of why and how.
We have to be careful, because of our minds and mouths can be very sharp, of what we fight for and against. I choose to not fight against religion, but for science and reason. These are the fights that will end discrimination and ignorance.
Look, it hurts the reputation of atheists and scientists when atheist scientists like Dawkins go on their own crusade against what others believe. It makes us look very bad, and it decreases our ability to fight for good in our society. There are more responsible ways to go about dealing with religion than militant atheism. I hope you see that now.

The separation of church and state should result in religious freedom for all and imposed or forbidden religion for none. Here in North America, it seems that people think that it means removing any influence of Christianity from the entire culture, sparing only private homes and places of worship. This is not the role the separation of church and state was designed for. “Political correctness” would have us believe that any public mention of Christianity is to be outlawed; that just admitting in public that one is a Christian is offensive. Jesus commanded us to be salt and light to the world. He didn’t set Christianity up as the world government (although He will do so during the Millenium – see Revelation 20), but He told us not to hide our light. God forbid that we should develop the total separation of church and mind.
The thing is, not everyone believes that Jesus commanded us to do anything. Some people believe that if they don’t beat their wife, Zeus will fry them with lightning. The only way all viewpoints/faiths can live in harmony is to be completely separate from the people who make decisions in government.