One of the problems faced by atheism is, even if we work under the assumption that atheism is rational, most people in the world are not fully rational, not is anyone rational 100% of the time. Rather, we also live in the subjective realities created by the free market, advertisers, media, culture, fads, fashion, gangs, philosophies, human nature, instincts, etc.
For example, the hype around a new product, when the old one has not wore out, is not rational, but is based on emotional appeal. Sitting in line for a week to get tickets to a concert is fun at emotional level but is anything but rational. What becomes of the irrational atheists who will appears, who will be the majority of the people and the majority of the time. How does atheism bring this to the future, with so many external and internal forces neutralizing reason, for fun, profit, power and impulse? Religion is geared to this aspect of humans, just as atheism is geared to science and reason. Does atheism have its own agenda in terms of control over the subjectivities of the majority so it can reach the atheist ideal of reason?
Atheism can currently cherry pick birds of a feather, but what happens if it inherits all those majority of humans that are not quite as rational, including those who like to manipulate the irrational, as well as those who enjoy impulse?
Would atheism teach people the art of media manipulation to they can avoid it and not become an irrational atheist? Or would it simply take advantage of this tool to do its own manipulation? Just voiding the concept of God does not equal rational. That conclusion is irrational. Would human nature, in conjunction with atheism, simply take advantage of this opportunity for control? What would that world look like; Stalin, which needs to censor competition, like it already tries to do, or could it still allow for the paradox of majority irrationality?
A good analogy is the chess club. All the students like chess and all have this in common. They might lament how it would be nice if all the students played chess, since it would strengthen the mind. They finally come into power and try to teach the joy of chess, only to have the jocks give them a wedgie. The party hounds are too buzzed to learn. But being in power, do they allow for these differences or do they form a police state to re-educate? The pressure and frustration can cause even the rational to act on irrational impulse; irrational atheism.