The answer, at its deepest level, lies in the very fact that they have repudiated the religion they scorn as irrational. Religion, or more precisely the religion of the Bible, and more precisely still the Judaism at its core, is the real crucible of reason. Those who reject the religion of the Bible are rejecting reason itself.

So why do I make this counter-intuitive suggestion that Judaism gave rise to rationality?

The popular belief is that the roots of reason and science lie in ancient Greece. Now undoubtedly Greece contributed much to modernity and to the development of Western thought down the ages. Nevertheless, in certain crucial respects Greek thinking was inimical to a rational view of the universe. The Greeks, who transformed heavenly bodies into gods, explained the natural world by abstract general principles.

By contrast, science grew from the novel idea that the universe was rational; and that belief was given to us by Genesis, which set out the revolutionary proposition that the Universe had a rational Creator. Without such a purposeful intelligence behind it, the universe could not have been rational; and so there would have been no place for reason in the world because there would have been no truths or natural laws for reason to uncover. Science could only proceed on the basis that the universe was rational and coherent and thus nature behaved in accordance with unchanging laws. 

The other vital factor was the Bible's linear concept of time. This meant history was progressive; every event was significant; experience could be built upon. Progress was thus made possible by learning more about the laws of the universe and how it worked. 

It is atheism, in fact, that is innately hostile to reason. Instead of worshipping God, man worshipped man. To be more precise, man's ideas became the articles of faith. But instead of wrestling with God, man's ideas brook no dissent, no argument. That's because they are not actually ways of making sense of the world, of asking the great questions of why am I here, what is the purpose to my life, how should I behave in ways that give my life meaning. The ideas that man worships are instead ideas he invents to gain power over his fellow human beings. They are ways not of explaining the world but of controlling the world. Therefore they cannot be resisted or argued against. There cannot be any alternative set of propositions. There cannot be any debate. They are a doctrinal belief system of power.

Indeed, atheism has given us through such ideologies a faith which repels reason. Ideologies such as environmentalism, or the belief in the innate harmony of the natural world; scientism, or the belief that everything in the universe has a scientific explanation; moral relativism, or the belief that everyone's value system is equal to everyone else's; multiculturalism, or the belief that no culture can take precedence over any other; egalitarianism, or the belief that everyone is entitled to identical outcomes regardless of their behaviour. These all repel reason because, instead of looking at evidence to reach a conclusion, they start with the governing idea and force the evidence to fit it.