No atheist should expect to convert the religious by means of rational argument. Religions (as well as many other ideologies such as Randianism or political Libertarianism which don't specifically reference "God") are by definition hermetic, more-or-less logically valid (but hardly sound) and predicated on blind faith, i.e. unfalsifiable and therefore not dependent on evidence.
In most Western societies, its each person's political right to have whatever blind faith he or she chooses, or no blind faith at all, without fear of official prosecution or unofficial persecution.
Similarly, engaging in rational argumentation—which presumes sensitivity to evidence—with the religious about their religion is an exercise in futility. The decision to evaluate one's own beliefs in light of the evidence of the senses or metaphysical criteria such as Occam's Razor must start inside the individual's own consciousness: One cannot even persuade—much less force—an individual to make that first step.
Once that first step has been taken, of course, one can engage in rational argumentation; it's noteworthy that almost all theists who begin to evaluate their beliefs in the light of evidence and Occam's razor end up as atheists, usually quite vocal and uncompromising atheists. (It's also noteworthy that most atheists who convert to theism seem not to have ever valued evidence and rational argument to begin with.)
I think that most atheists recognize this futility. I don't think that very many atheists try to argue the committed religious out of their beliefs (or they soon learn the futility of doing so and stop). Rather, when atheists talk about religion, there are two other goals in mind.
The first other goal is to simply demonstrate the rational vacuity of religion to those who have taken the first step, but are often so insulated that they are simply unaware of alternative modes of thought. Note that almost all religions strongly disapprove of even allowing their adherents even exposure to alternative modes of thought.
The second goal is stop the fraud. All you have to do to justify your blind faith is call it "blind faith" and invoke the First Amendment (or, outside the U.S., the uncontroversial principle of freedom of thought). Even if your blind faith affects how you operate in the physical world, one can justifiably prosecute and persecute you only for the physical effects, not the underlying blind faith.
It is, however, the representation of religion as knowledge, as reasonable, as rationally, evidentially justified that the nonreligious decry as fraud. It is an attempt to infringe, as it were, on Gould's magisterium of science. It is the attempt to co-opt the authority of rationality for the purpose of religion.
This effort is objectionable on two points: First, is it internally contradictory: A rational, reasonable belief is, by definition, contradictory to blind faith. You cannot both claim the epistemic authority of reason and the political authority of unreason. More importantly, the effort to co-opt reason in the service of religion corrupts reason. Reason is privileged because it always gives the same answer for everyone. To use reason to justify idiosyncrasy—and unfalsifiable beliefs are always, to some degree, idiosyncratic—necessarily corrupts this "same-for-everyone" characteristic.
Blind faith as blind faith has to be protected, because Metaphysical Naturalism itself cannot be rationally justified to the exclusion of other metaphysical systems without circularity: Metaphysical Naturalism is rational justification itself. But by the same token, Metaphysical Naturalism deserves its own integrity; you're free to reject Metaphysical Naturalism, but you're not free to redefine it and co-opt its authority. To do so is fraud and lies.
Be religious if you choose. Proclaim your religious beliefs (in, of course, a civilized and appropriate manner) to your heart's content. At worst, if you call for some actual action I consider objectionable, I will object to the action.
But proclaim your religious beliefs as reasonable, and I'll be right in your face calling you a liar. You can have your blind faith, but I have my reason, and I'll fight to protect it.