On many occasions, opinions that aimed to uphold government religious speech against Establishment Clause challenge have stressed that such speech was "nondenominational," or have argued that the Establishment Clause bars discrimination among religions — even in government speech — but not discrimination in favor of religion generally.
But this was always something of a fiction. Every reference to "God" carries a theological view that excludes not just atheists but also polytheists (such as Hindus and Shintoists) and religious people whose religious views don't involve a God (such as Buddhists). There are no nondenominational religious statements, except perhaps in jokes of the "whoever You are, male, female, neuter, animate, inanimate, many, one, existent, or nonexistent" variety.
To his credit, Justice Scalia's dissent in McCreary acknowledges this, suggests a dividing line (endorsement of monotheism is fine, endorsements of specific monotheistic religions is not), argues that this line is supported by original meaning and history, acknowledges that this may offend people who adhere to nonmonotheistic religions, but argues that this shouldn't pose a constitutional problem. Yet the liberals rightly ask: Why does this history so clearly support a constitutional preference for monotheism (which includes Christianity, Judaism, and Islam) but not for Christianity specifically?
Scalia points to a good deal of historical evidence (in my view very powerful evidence) that the Framers and subsequent generations endorsed some government religious speech. And he explains his "monotheism" rule by pointing out that the speech generally referred to "God" or versions of that, and not "Jesus Christ."
But there were quite a few contemporaneous state constitutions that preferred Christians over non-Christians (some preferring Protestants over non-Protestants). There was influential commentary in the 1800s saying that the Constitution tolerated endorsement of Christianity specifically; and Justice Scalia has long stressed the importance of post-enactment interpretations as well as of the original meaning. More broadly, when Christians talk about "God," they may be doing this not because they understand there to be some "endorsement of monotheism OK, endorsement of Christianity forbidden" rule, but because their Christian theologies (or even their esthetics) leads them to use the term "God" in certain contexts more than the term "Jesus Christ."
Jack Balkin cricitizes Justice Scalia on this score, and while I don't entirely agree with his views, it seems to me there is much to them. Certainly an originalist may well conclude that, whether he likes it or not, government endorsement of Christianity is permissible. But Justice Scalia's position that the Establishment Clause tolerates endorsement of monotheism but not of Christianity, while more palatable to many today (likely including Justice Scalia himself), is also less persuasive as an originalist matter.
UPDATE: Rick Garnett defends Scalia at SCOTUSblog.