Kurtz emphasizes the positive point of departure of philosophical naturalism in all its dimensions. He advocates the scientific method, but cautions against methodological reductionism (a.k.a. physics envy). Note Kurtz's exposition of ethical naturalism. All in all, Kurtz wants to emphasize the role of naturalism in constructing the good life.
OK so far . . . one point, though:
"Scientific methods grow out of the practical ways that people cope with the world and solve problems: as Dewey pointed out, they are continuous with common sense."
I think this is quite mistaken; scientific theorization (along with philosophical reflection and critical thinking) is quite the opposite of "common sense".
It's not clear whether the "New Atheists" are being used as a foil here. In the end, Kurtz criticizes Sam Harris for recommending that atheists (etc.) go under the radar, which is different from accusing them of negativity.
My overall discomfort with this piece is that Kurtz abstractly fights the battle for the Enlightenment, but has nothing of analytical value (i.e. scientific) to say about the society we live in beyond these general platitudes. His philosophical preaching is devoid of concrete political and social content. Also, his brand of naturalism can play a number of ideological and political roles; there is no guarantee at all that "naturalism" so vaguely formulated would be used to intelligently analyze society or intervene in its politics. It's sad that after all these decades, Kurtz has so little to say.