Sam Harris and Andrew Sullivan agree that the biggest issue that we face today is "fundamentalism". Fundamentalism of any stripe, Islamist, Christianist and neo-conservative, threaten sensible, intelligent people of any ordinary political persuasion, liberals and conservatives (at least conservatives like Sullivan).
There will always be a core of people who are going to embrace some sort of fundamentalism. Fundamentalists can be effective, however, only if they can persuade a fairly large number of people who are not "naturally" fundamentalist to support their programs. Just as the core of truly fundamentalist Islamists have persuaded millions of otherwise peaceable and tolerant moderate Muslims to support or at least tolerate their activities, the core of truly fundamentalist neo-conservatives and Christianists have persuaded millions of otherwise peaceable and tolerant moderate conservatives and moderate Christians to support or at least tolerate their own programs--at least through the first six years of George W. Bush's presidency.
It is precisely the sort of epistemic vagueness, confusion and indecisiveness we see in religious moderates which renders them susceptible to persuasion by fundamentalists. When fundamentalists claim to know the truth, moderates are left without a principled response because they don't have a clear, rigorous, principled method for evaluating the truth of religious or moral statements--for knowing religious and moral truth.
Of course religion is not the only source of epistemic confusion. But there are two reasons why I think religion, especially moderate religion, deserves special attention in this kind of debate. First, although religion doesn't have a monopoly on the kind of bullshit which preys on epistemic confusion, historically it's far and away the biggest and most prominent supplier.
More importantly, religions, especially the Abrahamic religions, rest on scriptures that were created during extremely authoritarian, oppressive and violent eras of human history. These scriptures were created in eras when activities considered today to be obvious moral evils--wars of aggression and conquest, slavery, oppression of women, absolute monarchical authority--were commonplace and unquestioned. There can be no doubt that a literal reading of these scriptures, even the Christian New Testament, support these moral evils. Moderates will thus always be at an enormous disadvantage trying to employ scriptural authority: Fundamentalists need only point to the text; moderates have to invent all sorts of fanciful hermeneutics to extract a modern morality from these scriptures. One cannot help but think it is fundamentalists who are at least being more intellectually honest: They at least assert (usually) that the Bible means exactly what it says; moderates seems all too often to claim the Bible means the opposite of what it says.
By lending scripture any authority, religious moderates fail to undercut the fundamentalists' moral basis. And, since fundamentalists can use scriptural authority better than moderates, lending even a little bit of authority to scripture can only support fundamentalism. Rhetorically, as well the moderates' wishy-washy responses fall flat next to the fundamentalists' confident certainty.
Religious moderates cannot just eliminate scripture entirely. Without scripture (or at least some sort of authority), one's beliefs about God cannot be anything more than pure individual conscience. Moderates appear to be even more uncomfortable with such relativism and subjectivism than they are with fundamentalism.
Talking about "doubt" is just another way of talking about what it means to know something. Because scientific doubt is both clear and testable, scientists are clear about what they mean both when they claim to doubt a statement and when they claim to know it. If one scientist says he knows something, we can rationally evaluate whether he really does know it, independently of whether we like or dislike the content of what he claims to know.
Lacking a clear notion of doubt, though, the religious moderate can answer the fundamentalist's assertion of certainty only with, "Well, you can't really know anything at all," (i.e. nihilism) or with, "Well, I personally disagree," (i.e. relativism). If ethics really is a matter of truth, not opinion, and if ethical truth really does have a religious foundation, then the half-hearted nihilistic "doubt" of religious moderation does nothing except to strengthen fundamentalism.
 To be fair, there is no lack of this sort of epistemic confusion on the left, which renders liberal moderates just as susceptible to persuasion by leftist fundamentalists. It's interesting, though, to note that "leftist" fundamentalist totalitarianism has prospered best in Russia and China. One can reasonably conclude that Russian and Chinese totalitarianism is due as much or more to their their well-documented history of authoritarianism in general--and the concomitant lack of resistance to argument from "scripture"--as to any inherent fault in leftist ideals.
 Of course, even soi disant fundamentalists engage in their own fanciful hermeneutics. It's risible to imagine Jerry Falwell or Pat Robertson taking Matthew 19:21 literally.