There are 2 aspects to atheism that one must examine. The first is the belief, or rather lack of belief, in God, chalilah. This post won't address that. The existence of God is provable by logic and philosophy and is addressed by far better authors than me so I won't go into that right now.
The second aspect is the motivation of atheists. Many, I'm sure, are quiet types who don't believe, don't care that they don't believe and don't care that others do believe as long as those others don't show up at their door with pitchforks and flaming torches.
Others, however, are quite militant about their atheism. Folks like Richard Dawkins, Christophen Hitchens and others not only don't believe but are genuinely perturbed by those who insist on continuing to believe after hearing all the arguments against it. Again, when confronted with rational counterarguments (usually offered long after the militant atheist in question has left the building in order to avoid a blow-up) most of their positions fall through. But we must step back and consider what motivates them.
One of the simplest rules in the business world is that if you're doing a good job your loyal customer base will stay with you even in the presence of competition. In the presence of stiff competition your business then has to up its game in order to remain viable but your customers will still give you a chance if they see you're adapting to the new market conditions.
If we extrapolate this to religion we can see this very model at work and perhaps this can explain why militant atheism has had such a strong rise in the last few decades.
For millenia a religion's only real competition was another religion. As a result all your religion had to do was promise some unique feature available only to followers in order to retain them. Chrisianity promised you Heaven if you believed in their saviour. Islam promised not to slaughter you if you accepted their prophet. Judaism promised you tzimmes and humentaschen along with a fierce defiance of history's tendency to wipe up small nations.
With the rise of Western intellectualism along with the rise in economic status of the average citizen of society all this changed. At one time you wanted to be a part of the big picture because that was the only way to matter. Now that people had their own homes, cars and stocks a rise in the status of the individual became paramount. Despite JFK's great speech people have, over the last few decades, been far more interested in what the state can do for them then what they can do for that state.
And religion's response? Tepid at best. People wanted a belief system without any accompanying obligations and religion offered the exact opposite. Just ask Frank Schaefer, a Methodist minister in the United States who was recently defrocked by his parent church organization. Despite clear rules against it he conducted the marriage rites at his son's gay wedding. His response to the defrocking is typical of modern Western attitudes. He doesn't think he did anything wrong, he doesn't think he broke any rules because the rules he broke aren't fair (according to him) and he won't accept being defrocked because, well because he doesn't want to. He simulatneously refuses to recognize the authority of his church while insisting on remaining an official within it.
What has this to do with the rise of atheism? Well part of it, I would guess, is a sense of authenticity. The bottom line for folks like Schaefer is that their god is a personal one. The deity, whatever they call him these days, agrees with their personal views 100% of the time. What they think is right, He thinks is right. Perhaps without realizing it they are worshipping themselves, each man a religion unto himself. An intellectually honest person would call them out on this and point out that since they don't have an external, objective source of divine revelation in their lives they are really atheists themselves.
The other is harder to deal with.In his essay "The Pangs of Cleansing" Rav Kook, ztk"l, writes that atheism is a response to religion that has gone off the rails. It is a challenge to a religious order that is no longer doing what it is supposed to do. Instead atheism arises and tries to fill the moral void that religion has left behind.
When we look around at our world we can easily see that this is what is happening. Every day it seems another scandal erupts either within the Orthodox community, the Catholic church or somewhere in the Dar al Islam. Religion, which should be a force for moral improvement and the advancement of human decency, seems to be the vanguard of a new Dark Ages and happily so. Is it any wonder people are making the simple equation and leaving religion, along with God, behind?
Therefore it behooves us not to be annoyed with the existence of militant atheism but to instead see it for what it is: a symptom of our illness as a religion and a call to improve ourselves. Should we do that, should we be able to restore Judaism as a consistent, moral order it would solve this problem and bring our final redemption that much closer.