I've dealt already with the argument that the NCSE website's funding by the National Science Foundation violates the Establishment Clause, and Francis Beckwith's article really makes no new points. But I have a few more thoughts about it--and about the sloppy thinking it reveals (which is pretty common among creationists).
In Rosenberger v. University of Virginia, 515 U.S. 819 (1995), the University ran a program which gave students money to publish newsletters and magazines. But religious publications were not eligible. Students sued, arguing that this was discriminatory. The state argued that the Establishment Clause prohibited it from allowing religious publications to participate in the program, but the Supreme Court rejected that argument (albeit, in dicta). "[A] significant factor in upholding governmental programs in the face of Establishment Clause attack," said the Court,
is their neutrality towards religion.... The guarantee of neutrality is respected, not offended, when the government, following neutral criteria and evenhanded policies, extends benefits to recipients whose ideologies and viewpoints, including religious ones, are broad and diverse.... we rejected the position that the Establishment Clause even justifies, much less requires, a refusal to extend free speech rights to religious speakers who participate in broad-reaching government programs neutral in design.Id. at 839. Now, I think it's pretty obvious that the National Science Foundation's criteria for grants are religiously neutral. As I've pointed out, the NSF has given grants to such religious institutions as the University of Notre Dame and the University of San Diego. The criteria for such grants are wholly secular, and there is no reason why, if ID proponents could devise a genuine experimental or research program, they could not also qualify for such a grant. Were NSF to reject them for a grant on the grounds that they're doing bad science, that would be legitimate, wholly secular criteria, and would not therefore violate the Free Exercise or Equal Protection Clauses.
Rosenberger, in short, shows that even if the NCSE's website statement can be plausibly described as a "religious" statement--which some strongly, and pretty persuasively reject--it would still not qualify as an "establishment of religion" for the NCSE to use a government grant, so long as that grant is based on neutral, secular criteria (i.e., aiding school teachers in understanding and teaching science.)
Now, what's most troubling to me is that Beckwith's argument is very shortsighted. He is arguing that the Establishment Clause prohibits government funds from ever going to a private speaker who makes arguably religious statements. This is an extreme of separationism that only the most ardent leftist makes. It has been--I believe rightly--rejected in cases like Zelman v. Simmons-Harris, 536 U.S. 639 (2002), and the people who have argued that the Court ought to reject it have usually been the conservatives, who have argued that government should have more, not less freedom to fund the propagation of religious statements. Beckwith, relying (erroneously, as I've mentioned) on Justice O'Connor's separate opinion in Lynch v. Donnelly, 465 U.S. 668 (1984), argues that any time government funding goes to a private expression of religious views--even when filtered through neutral, secular criteria--it constitutes endorsement. But this would not only forbid school choice programs like the one upheld in Zelman, it would also prohibit government from giving grants to faith-based charities, from placing the words "In God We Trust" on the currency, from having a national Christmas tree, or from sending firetrucks to put out fires in churches. People have made plausible arguments for some of these positions, but it's surprising to see the basic premise of such positions propagated by a religious conservative.
Beckwith's argument is silly, shortsighted pandering based on a sloppy grasp of the caselaw. In fact, you encounter this quite often in the Establishment/Free Exercise realm. It's sort of the legal version of creationism--complete with quote-mining, context-dropping, mis-citations, legal fallacies, and conspiracy-theory-type thinking--and it's usually employed to flatter the preconceptions of one political constituency in particular. Just the other day on the way home, I heard Paul Harvey read a note from a listener, saying "Paul, why can't my kids read the Bible in school? They can read it in jail!" We're supposed to laugh bitterly at the decline and fall of decent, upstanding civic religion and the death of Norman Rockwell. But the fact is that nothing in the Constitution prohibits a student from reading the Bible in school, and in fact it would be unconstitutional (as well as against statutory law, in California) for a teacher to forbid a student from reading the Bible. (Of course, a student can't read the Bible if it's disrupting the class, or if he's supposed to be working on another assignment--but that's reasonable, isn't it?) Yet people gobble up this pseudo-witticism, because they know nothing about the law, and have been taught that the judges are part of a conspiracy against religion.
One more example. Not long ago I got a chain-email from someone complaining about Newdow v. U.S. Congress, 292 F.3d 597 (9th Cir.2002), the case about the pledge of allegiance. The note said that, by the logic of the opinion, the judges couldn't really be judges because they have to say "so help me God" in their oaths of office, so the judges were really saying their own oaths of office were void, and therefore their decision was really void, too. Aha! It's brilliant!--yet the phrase "so help me God" is not required of federal judges, and the Constitution expressly prohibits a religious test for federal office--and the text of the presidential oath excludes any reference to God, and allows people to "affirm," rather than "swear," in order not to limit the Presidency to a particular religious view! But these sort of--shall I call them "blankie memes," as in, security blanket?--these sorts of things really appeal to people who know nothing of the law.
I've said before, and I still believe, that scientific illiteracy is the greatest threat to western civilization; greater than Islamic terrorism, greater than drugs, greater than importing four-inch-long lobster tails. But I would put ignorance of the Constitution high on that list as well.