Is the "Is-Ought" Fallacy Really Fallacious?

Daylight Atheism, in discussing Sam Harris's controversial but insightful book, The Moral Landscape, argues we can step over the "is-ought" problem and I agree. Here's the money quote:
It's true that you can't take any catalogue of facts about human nature, however comprehensive, and from them distill the conclusion: "We ought to value human flourishing." But for the same reason, it's also true that you can't start with any catalogue of facts about human history or the world, however comprehensive, and from them distill the conclusion: "We ought to use the scientific method to study reality." Does this cast doubt on the legitimacy of science as a human endeavor? More importantly, does it imply that there exist other ways of knowing that are just as valid? No system of thought can be derived out of thin air. They all have to be based on axioms that can, in principle, be rejected. But if that's a strike against objective morality, it's also a strike against philosophy, science, mathematics, and every other branch of human inquiry as well....And what to do with those stubborn philosophical skeptics, who insist to their last breath that we can't prove that human well-being should be valued above other qualities? Let them be. If our approach to morality is correct, its superiority will be borne out in practice and people will eventually be persuaded to come along for the ride, just as theists switched from faith healing to antibiotics when they saw how much more effective the latter was. Link.