I've often argued that it's improper for the government to discriminate against religious people and institutions because of their religiosity (see, for instance, my Equal Treatment Is Not Establishment article). But it's equally improper for the government to discriminate against irreligious people and institutions because of their lack of religiosity.
Fortunately, such discrimination is, I think, rarer now than it once was -- recall that until 1961, some states officially excluded atheists from certain jobs, such as notaries public. Yet it persists in some contexts, even overtly, and it's important to condemn this. For instance, though it's an open question to what extent it's constitutional for the government to discriminatorily give religious exemptions from generally applicable laws to religious objectors but not conscientious objectors, I think that the government should treat religious and conscientious objectors evenhandedly even if it isn't constitutionally obligated to. (I set aside here the question of government speech; I think the case for a government power to express itself religiously, at least in some contexts, is much stronger than the case for a government power to discriminate among citizens based on religion, but that's a story for another day.)
Here's an example that I think is particular egregious: The discrimination in favor of religious parents and against irreligious ones, or in favor of more religious parents and against less religious ones, in child custody cases, on the theory that it's in the child's "best interests" (that's the relevant legal test) to be raised with a religious education.
Mississippi is the most serious offender, though I've seen cases since 1990 in Arkansas, Louisiana, Michigan, Minnesota, Pennsylvania, South Carolina, South Dakota, and Texas; there are similar cases in 1970s Iowa, Nebraska, North Carolina, and New York. (I give cites below.) In 2001, for instance, the Mississippi Supreme Court upheld an order giving a mother custody partly because she took the child to church more often than the father did, thus providing a better "future religious example." In 2000, it ordered a father to take the child to church each week, as a Mississippi court ordered in 2000, reasoning that "it is certainly to the best interests of [the child] to receive regular and systematic spiritual training."
This violates the Free Speech Clause: Just as government discrimination against religious viewpoints is unconstitutional, see, e.g., Rosenberger v. Rector, so government discrimination against nonreligious viewpoints is unconstitutional. It violates the Establishment Clause: It coerces religious practice, either directly by ordering a parent to take the child to church, or indirectly by threatening the parent with a diminution in legal rights if he doesn't practice religion; the Court has rightly and unanimously taken the view that legal coercion of religious practice is unconstitutional (see both the majority and the dissent in Lee v. Weisman). It endorses religion (though the prohibition on endorsement is more controversial than the prohibition on coercion). And it discriminates based on religiosity. It may also violate the Free Exercise Clause, if (as I think is the case) the "free exercise of religion" includes the freedom not to have one's rights reduced because one exercises religion solitarily rather than in church, exercises religion less actively and passionately than some others, or has no religion at all. (The freedom of speech has been understood as including the freedom to choose what not to say as well as what to say; it seems to me the same applies to free exercise of religion.)
Finally, I realize that some people think it's in a child's best interests to be raised in a religion, perhaps because it will be more likely to make the child feel deeply about the need to follow some moral code. For all I know, this might be true. But other people equally think it's in a child's best interests to be raised skeptical of all religions, because it will be more likely to make the child into a rational thinker who doesn't take factual assertions on faith, and refuses to believe such assertions (whether about the Virgin Birth or the parting of the Red Sea or the creation of the world by an omnipotent, omniscient, benevolent God) unless he's given solid evidence that they're true. Freedom of religion, and freedom of speech, means that the government shouldn't make custody decisions based on such assumptions -- and of course if it can make custody decisions based on anti-atheist assumptions, it can also make them (and has made them) based on antireligious assumptions.
Citations for discrimination against the irreligious or less religious: Blevins v. Bardwell, 784 So. 2d 166, 175 (Miss. 2001); Staggs v. Staggs, 2005 WL 1384525 (Miss. App.); Brekeen v. Brekeen, 880 So. 2d 280, 282 (Miss. 2004); Turner v. Turner, 824 So. 2d 652, 655-56 (Miss. App. 2002); Pacheco v. Pacheco, 770 So. 2d 1007, 1011 (Miss. App. 2000); Weigand v. Houghton, 730 So.2d 581 (Miss. 1999); Johnson v. Gray, 859 So. 2d 1006, 1014-15 (Miss. 2003); McLemore v. McLemore, 762 So. 2d 316 (Miss. 2000); Hodge v. Hodge, 188 So. 2d 240 (Miss. 1966); Johns v. Johns, 918 S.W.2d 728 (Ark. App. 1996); Ark. Sup. Ct. admin. order no. 15 (enacted 1999); Peacock v. Peacock, 903 So.2d 506, 513-14 (La. App. 2005); Pahal v. Pahal, 606 So. 2d 1359, 1362 (La. App. 1992); Ulvund v. Ulvund, 2000 WL 33407372 (Mich. App.); Mackenzie v. Cram, 1998 WL 1991050 (Mich. App.); Jimenez v. Jimenez, 1996 WL 33347958 (Mich. App.); Jonhston v. Plessel, 2004 WL 384143 (Minn. Ct. App.); In re Storlein, 386 N.W.2d 812 (Minn. Ct. App. 1986); McAlister v. McAlister, 747 A.2d 390, 393 (Pa. Super. 2000); Thomas v. Thomas, 739 A.2d 206, 213 (Pa. Super. 1999); Gancas v. Schultz, 683 A.2d 1207 (Pa. Super. 1996); Scheeler v. Rudy, 2 Pa. D. & C. 3d 772, 780 (Com. Pl. 1977); Shainwald v. Shainwald, 395 S.E.2d 441, 446 (S.C. App. 1990); Hulm v. Hulm, 484 N.W.2d 303, 305 & n.* (S.D. 1992); In re Davis, 30 S.W.3d 609 (Tex. Ct. App. 2000); Snider v. Grey, 688 S.W.2d 602, 611 (Tex. Ct. App. 1985); In re F.J.K., 608 S.W.2d 301 (Tex. Ct. App. 1980); In re Marriage of Moorhead, 224 N.W.2d 242, 244 (Iowa 1974); Ahlman v. Ahlman, 267 N.W.2d 521, 523 (Neb. 1978); Dean v. Dean, 232 S.E.2d 470, 471-72 (N.C. App. 1977); Robert O. v. Judy E., 90 Misc.2d 439, 442 (N.Y. Fam. Ct. 1977).
Citations for discrimination against people who are seen as too religiously fundamentalist: Collier v. Collier, 14 Phila. 129 (Pa. Ct. Common Pleas 1985); Waites v. Waites, 567 S.W.2d 326 (Mo. 1978); Stolarick v. Novak, 584 A.2d 1034 (Pa. Super. 1991); In re Marriage of Epperson, 107 P.3d 1268 (Mont. 2005).
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