I've just put up a new version of my forthcoming Stanford Law Review article on the subject; it has two whole new sections, on the Establishment Clause and on state Religious Freedom Restoration Acts. The issue, as before, is whether the government may limit a subsidy to groups that don't discriminate based on various criteria, given that the groups may have a constitutional right to so discriminate (in the wake of Boy Scouts v. Dale). I think the answer is "yes"; I'm not a big fan of the antidiscrimination rules involved, but it seems to me they are indeed constitutional, even when applied to ideological groups that have ideological reasons to discriminate based on religion, sexual orientation, sex, race, ethnicity, and the like. Interestingly, the strongest argument for exemptions for those rules comes not under the First Amendment, but under state Religious Freedom Restoration Acts (see Part VI of the article).
If you're up on the First Amendment or religious accommodation jurisprudence that touches on this subject -- and, better yet, the Court's jurisprudence on refusals to subsidize abortion, private schooling, and other constitutional rights, a jurisprudence that I rely on heavily in my piece -- I'd love to hear your views. I should say (realizing that beggars can't be choosers) that while there are lots of interesting broad philosophical issues that my topic touches on, I would prefer to get comments from people who have read (or at least skimmed) the paper, and who are up on the somewhat technical legal doctrines that the paper relies on.