"Yes, that is exactly correct: there is truth "out there", independent of us, and since I believe that atheism is among the catalogue of true things, I do believe that in that respect, only atheists know how to find it."

This delves into deeper levels of epistemology than I am capable of grasping, but I would say, rather than there being some "truth 'out there'", that instead we can know with confidence only that certain propositions are false. In fact that's what's really meant by the statement "atheism is true". What's really being said (by me at least) is that a large number of doctrines taught by fundamentalist christians are demonstrably false. And that's how science works. Our confidence, say, that the sun will rise tomorrow is based on past experience and the lack of any evidence to the contrary, although it's certainly possible that an as-yet undetected meteor could destroy the earth tonight. So I don't do experiments to prove things true, I do experiments to test hypotheses, understanding all the while that certain results may falsify my hypothesis. So yes I'm a huge fan of popper as well, what little I know of him.

"You rightly note that doubt is a fundamental virtue of science, but you miss the corollary: doubt must be coupled with confidence in the evidence. Otherwise, we just have a pointless, radical skepticism which forecloses the possibility of knowing anything."

I would rephrase that to say that my confidence in any given theory is bolstered by each piece of evidence which by itself held the possibility of proving the theory false. It's also the case that any given piece of evidence by itself should be suspect, so reproducibility is key. Newton's theory of gravity was fantastic, but was "false" in the thirteenth decimal place for example.

So there's mathematics and logic where you really can prove things "true", based on underlying premises, and then there's the physical world which is much more complex. If anyone ever figures out what the statement "quantum mechanics is true" means, I'd like to know about it. There are just so many things about reality that seem completely nonsensical, like entanglement and all kinds of strange stuff.

But indeed I believe the statement "the sun will rise tomorrow" is true.

GD

This part of the article sums it up perfectly: "What I cannot countenance is the smug belief of some people that they can win the debate by not showing up."

On a more serious point, I understand that it is very tempting to ridicule theists beliefs (I can barely resist sometimes), but we must try. If you want people to listen to your point of view don't start by insulting them. You've made it confrontational and the pride-penalties for conceding or even listening have been increased.

We should try to ask searching questions rather than tell people what's wrong with their beliefs and characterize them badly.

It depends on the situation and the audience. If you are with a smallish group of people, who are willing to listen to you for an extended period of time, then of course you approach the discussion in a calm reasoned fashion.

But that is a luxury position. Often one only has a few words or a few seconds, and then it is far more likely to get attention simply to point out that a particular belief is ridiculous, or that a particular theist is a liar.

Ask yourself: did the religious right get where it is in America by reasoned argument? Of course not! There is a (large) group of people which is susceptible to argument by insult and sometimes it may be necessary to reply in kind.

You can use the names of other popular gods, e.g., if you are debating a Christian you could use Vishnu, etc., or versions of what is alleged to be the same god (e.g., Allah of the Muslims vs God of the Christians).
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Re Jonas' (J) article, some thoughts:

Jonas does not acknowledge that some faith-based crimes have been of macroscopic proportions.

Jonas fails to cite a single example of a “macrocosmic” “faith-based mystery, beauty or wisdom,” much less one that is not equally-matched if not surpassed by one that is not religiously-based.

J: “There's a big difference between knowing there is a God (the deist position), not knowing if there is a God (the agnostic position), and knowing there is no God (the atheist position).”

Here Jonas demonstrates that he has not understood the positions at issue. Hitchens’ is not primarily criticizing Deism; he is criticizing specific theisms, e.g., the main ones today being Christianity and Islam, but also some of the others and polytheism. Secondly, Jonas mischaracterizes the atheist position as “knowing there is no God.” In fact, the most common position among atheists is lacking a belief in god or gods, on the grounds that there is no support for the belief and therefore no grounds for having the belief. What Jonas seems to be referring to is the “strong” or “positive” atheist position. However, this doesn’t necessarily mean that the atheist claims to know that God does not exist; rather, the strong atheist may, on the basis of some analyses and evidence, believe that god does not exist. There is a difference between having a belief and having knowledge. Scientists distinguish between theories and facts.

Another problem is that Jonas, like most, characterizes the whole issue over god’s existence as a purely philosophical debate. However, that need not be the case. Questions of existence are first and foremost in the domain of science. To claim that God exists is claiming something much more than that it exists in one’s mind as an idea. Rather, it is a claim that God exists in reality as a thing or agency outside of (or at least in addition to) people’s minds. Such claims about god’s existence require physical evidence. In other words, claims of existence are at least postured as scientific. In science, the burden of proof is on the one who makes the claim. Someone who claims that God exists ought to be able to specify the conditions under which God could be detected scientifically. If theists are unable or unwilling to do this, they cannot use the non-result of an experiment that never took place as justification for maintaining their belief in God’s existence. At the very least, believers have no basis for going beyond the belief that God exists as an idea in their heads; that God exists as an idea in people’s heads is something with which most atheists would probably agree.

J: “Of the three, two debate from an assumption of knowledge (the deist and the atheist) and one from an acknowledgment of ignorance (the agnostic). Because neither the deist nor the atheist can possibly know, they both operate from a delusion. Only the agnostic, who demonstrably does not know, has his feet on terra firma.”

For the moment, let’s take 'delusion' simply to mean mistaken belief. There is no evidence that atheists are delusional in lacking a belief in god or, in the strong case, having a belief that god does not exist. To show that atheists are delusional, physical evidence would have to be presented that (a) the atheist has been presented with the very strong scientific evidence of god's existence (as more than an idea in people's heads), and (b) the atheist rejects and continues to deny (a). Jonas has presented no such evidence of (a) or (b), and thus has no basis for claiming that the atheist is delusional. Indeed, if Jonas is agnostic, he must remain agnostic as to whether either believers or atheists are delusional. Yet the belief that god exists as more than an idea in people’s heads is a delusion if no supportive scientific evidence supports it. That is because as a general principle it is mistaken to believe something for which there is no evidence (e.g., the principle by which, I would venture, Jonas is not agnostic with regards to Quetzalcoatl).

Jonas also fails to distinguish between different degrees of belief or doubt. This again reflects the stubbornly non-scientific attitude of dealing in idealized absolutes, i.e., that people are either 100% sure that God exists, 100% sure that he doesn’t exist, or 100% uncertain about the whole issue. None of these are representative of scientific positions on the question of God’s existence. If we have even a small amount of evidence that people made up all the particular gods proposed thus far (at the very least we know people can create them; even toddlers can invent them too), whereas there is no evidence that god exists as more than ideas in people’s heads, the evidence clearly supports the atheist position more than the others.

To show that agnostics are not mistaken, i.e., not delusional, also requires a scientific study. However, the gods about which agnostics tend to be agnostic tend to be gods that are so ill-specified that there is no possible way to test claims about their existence. Agnostics generally will not tell you that they are agnostic with regard to the flying spaghetti monster, Zeus, virgin births, and various other miracles, etc. Agnostics are suspiciously agnostic to the extent that the deity in question is unspecified or ill-specified, ever-conveniently out of the reach of science. Thus, agnosticism becomes difficult to distinguish from obscurantism. Loosely, one may be said to be “agnostic” with regard to the contents of unintelligible gibberish, but that is not the same as being agnostic with regard to some reasonably well-specified god.

Still another major problem for agnostics has to do with morality. Are agnostics agnostic with regard to the propriety of putting blasphemers, apostates, adulterers, and disobedient children to death? Are they agnostic about divine-text-commanded wars to establish a religion and force conversions? Are they agnostic about divine permission to rape female captives and slaves? The agnostic may try to avoid these problems associated with specific religions by appeal to that comfortable retreat, the ill-specified deistic god. But is divine command itself—even if we grant the existence of the deity for the sake of argument—a plausible basis for morality? Is the agnostic agnostic with regards to the propriety of divine command per se?
Jonas says there are believing and unbelieving fools—though apparently no agnostic fools! However, whether or not anyone is a fool is besides the point. The issue Jones raised, and then avoided, was over whether the particular gods proposed thus far exist or not.

Doubt and uncertainty are fundamental virtues of scientists and the scientific method specifically, but statements like this foster the illusion that there's a "truth" out there somewhere and only atheists know how to find it.

Yes, that is exactly correct: there is truth "out there", independent of us, and since I believe that atheism is among the catalogue of true things, I do believe that in that respect, only atheists know how to find it. You rightly note that doubt is a fundamental virtue of science, but you miss the corollary: doubt must be coupled with confidence in the evidence. Otherwise, we just have a pointless, radical skepticism which forecloses the possibility of knowing anything.

Speaking as a former fundamentalist now rational scientist, I do know that the more you know, the more you know you don't know.

When we learn more, we do become aware of how many more facts are yet to be known, I agree. That does not take away our knowledge of the facts we do possess.