First off, there's atheist victimology: Boohoo, everybody hates us 'cuz we don't believe in God. Although a recent Pew Forum survey on religion found that 16% of Americans describe themselves as religiously unaffiliated, only 1.6% call themselves atheists, with another 2.4% weighing in as agnostics (a group despised as wishy-washy by atheists). You or I might attribute the low numbers to atheists' failure to win converts to their unbelief, but atheists say the problem is persecution so relentless that it drives tens of millions of God-deniers into a closet of feigned faith, like gays before Stonewall.
Mike Dunford's response to this is quite right; one test of such a statement is whether it can survive a process of minimal analogy. Take the first sentence and substitute other things for it: Catholic, Jewish, Mormon, etc., changing it as little as possible. See whether the analogue is bad. That's not a test for truth, but it's a good practical way to establish one's ethical obligation to show that there is a fundamentally significant difference involved here, to show that, in fact, this rhetoric is appropriate to atheists in ways it's not appropriate to the analogue cases. This has to be shown for the claim to have any feet; and because of this, at the very least, we have to show some recognition that it needs to be shown. We don't find this here.
A second issue, and Mike Dunford rightly brings this up as well, is that we should be careful not to paint all atheists with the same brush. In fact, atheists are an extraordinarily diverse group. Some atheists no doubt fit Allen's description, but others certainly do not. And Allen would have been wiser to pick a single issue, and a single set of atheists, and actually give reasons. Without this, she is merely arguing on her own presumptions and vague impressions. In casual speech, or in other kinds of informal forum, we can sometimes allow a bit of looseness on something like this; but this is the sort of thing that could easily have been made more precise before it ever came to publication.
There are bits and pieces of things that could be shaped into arguments in Allen's piece; she doesn't bother, and thus wastes an opportunity for reasoning on jumbled rhetoric.