There's a pernicious style of argumentation among many secularists. You see it in the works of the New Atheists, you see it in this piece by David Brooks justifying the coup in Egypt—and, if you do the right substitutions justifying every possible coup; Pinochet or the return of the Shah, anyone?—and, in a recent series of tweets from Joyce Carol Oates. These are only examples. I hear it from students. I hear it from people who take themselves to be educated and enlightened. It is very much in vogue among a certain set.
The argument—I guess it is really a claim substituting for an argument—is that religious believers are mentally defective, delusional, incapable of rational thought; or, that they are immoral, necessarily misogynistic, barbaric. And, because of this, one cannot trust them to teach or govern or take any other important roles.
Sometimes this strategy is aimed at all religious believers indiscriminately. Sometimes only at those one particularly disdains. Usually, these days that means Muslims.
I have an interest in the survival of secular government. And, Islamists scare the hell out of me; I know what happens to me in their ideal state. Pace some particularly strident thinkers—Sam Harris and Niall Ferguson come to mind—I think that there is a difference between Islam and Islamism. But as an accused member of the Homosexual International, and as a philosopher, I have no doubt that Islamism and its parallels in Christianity and Hinduism and even in Buddhism some places must be opposed and defeated, not least because I get killed in many of those views.
But you can't do this practically or while maintaining intellectual honesty, by claiming that all serious religious believers are defective in someway. Secularism needs defending, but it needs defending on its merits, not through ad hominem or through a baseless assertion that secularists and atheists really just are better.