Ah, but I think therein lies the real difference with New Atheists and those with an outlook more like yours.

They see the harm caused by fundamentalist assholes who are textural literalists, and say: this is bad, this is wrong, and this is cause enough to critique the whole religion with gusto. For there is no sensible reason why "textural literalism" shouldn't work. That it doesn't is a terrible condemnation of the entire enterprise.

To a New Atheist, theism isn't just building on sand, it's building on shrapnel mixed with dynamite.

The reason why the New Atheists are wrong--and I have reluctantly come to agree that they are--is much more subtle. It's not that people have some subtle interpretation that connects them with a feeling of transcendent wonder, or anything like that. Again, this just begs the question: why have that rotten literal text to begin with? Why not just have a morally and scientifically sane document at the outset and not need to rationalize away all the insanity, and then pretend it's some great boon to mankind?

The reason is that they're wrong in-a-sense is that people mostly don't use reason to begin with to guide their actions. The literal meaning of the text is a red herring anyway (despite the non-negligible number of people who end up taking it literally anyway). Rather, the text is an aide, interpreted in a collective context with our moral intuitions. (See In Gods We Trust by Scott Atran and The Righteous Mind by Jonathan Haidt for more support for these ideas.) All the nonsense--according to Atran anyway--serves to robustly signal group identity, because really, who would even think of something as convoluted and nonsensical as the Doctrine of the Trinity unless they were part of the Christian in-group? And our moral intuitions for the most part keep us behaving well even if the text exhorts us to do anything but (or is wildly inconsistent about what it exhorts us to do).

So, anyway, I think you're mostly not on the right track about what's going on here. Most of the New Atheists don't even argue what you're saying they do--that is, that in a strict sense no good can come from religion--but rather that if you tossed the primitive superstitions out, it would be uniformly better. (I grant that acolytes of the New Atheists do tend to adopt the straightforward "no good" approach.) I also have not encountered anyone who claims that all the problems of the world come from religion, only that many do.

I think New Atheist types tend, on average, to be plenty intellectual, to grasp complexity (maybe not in the case of the badness of religion, since they don't think there's complexity there), and so on. The difference is in how they understand the place of rationality in guiding human behavior. You sort of get at this in your article, and I agree with pretty much all of the points that you make there, but I don't think you quite put your finger on the issue as I understand it (at least not in a way that I recognize).

New Atheists overestimate the causal force of rationality. That is, if you take a literal reading of religious texts, you will find rational cause for all manner of atrocities. If you look at the actions of the religious, you will find all matter of atrocities put into practice. And yet, ironically, the former mostly does not cause the latter.

In some cases the former does cause the latter, and those cases deserve to be roundly criticized, and we could debate whether the too-common error of taking a too rational approach (i.e. too literal) to religions renders most religions too dangerous to accept as part of a civilized society. (For instance, we tend to recognize that gambling, especially in certain contexts, causes behavioral errors in humans so often that we decide, rightly I think, that access to gambling should be restricted.)

But the core argument, made most forcefully I think by Sam Harris, that the former leads to the latter is wrong because people mostly don't work that way. Under most circumstances (i.e. those not exquisitely tuned for rational deliberation), it works as follows: first, people's moral intuitions suggest a course of action. Then, their logical brain kicks into gear and finds a communicable rationalization for that action consistent with their religion. (You want your religion to be a confusing mess of contradictions for this to work, because then you're more likely to have support for whichever action you're arguing for.)

I am reluctant to blame the New Atheists for the oversight. It is profoundly non-intuitive that things work this way, but psychological experiments seem to verify that this is the normal mode of operation. It is even more non-intuitive to people who have carefully trained themselves to hone their ability to put rationality more into the driver's seat (e.g. by practicing the scientific method, by holding beliefs tentatively, by requiring an objective justification for a belief or action, etc. etc.).

And I certainly wouldn't charge the New Atheists with being intellectually impoverished as a whole. Dennett is about as erudite as they come, popularizers necessarily have to simplify somewhat, and every group has rabid supporters who don't think. If anything, I'd be more inclined to charge them with being emotionally impoverished, and thereby overestimating the power of intellect to govern others' behavior.

But if so, that's not so bad. More high-quality evidence about human psychology stands to change their minds. (Or, more high-quality evidence will demonstrate that my suspicions are wrong.) I'm not so sure we can say the same about the deeply religious.