It goes beyond mere “acknowledgment” of religion because its sole purpose is to encourage all citizens to engage in prayer, an inherently religious exercise that serves no secular function in this context. In this instance, the government has taken sides on a matter that must be left to individual conscience. “When the government associates one set of religious beliefs with the state and identifies nonadherents as outsiders, it encroaches upon the individual's decision about whether and how to worship.” McCreary County, 545 U.S. at 883 (O’Connor, J., concurring).
Like Michael Newdow's challenge to "In God We Trust" on U.S. coins, the Freedom From Religion Foundation's lawsuit against the Day of Prayer might be justified on a purist 1st Amendment theory about the establishment of religion.
But there is a doctrine in the law known as "de minimis," from a Latin maxim that basically says that government officials shouldn't concern themselves with trivialities. The National Day of Prayer is a pretty good candidate for the "de minimis" rule.
Not throwing a constitutional fit about what is sometimes called "ceremonial deism" makes it easier to oppose serious breaches of the wall of separation, like official prayers in public schools. In the culture wars, as in real ones, sometimes you need to choose your battles.
