The Supreme Court has recognized atheism as equivalent to a “religion” for purposes of the First Amendment on numerous occasions, most recently in McCreary County, Ky. v. American Civil Liberties Union of Ky., 125 S.Ct. 2722 (2005). The Establishment Clause itself says only that “Congress shall make no law respecting an establishment of religion,” but the Court understands the reference to religion to include what it often calls “nonreligion.” In McCreary County, it described the touchstone of Establishment Clause analysis as “the principle that the First Amendment mandates government neutrality between religion and religion, and between religion and nonreligion.”
The court ruled, in other words, that for the purposes of the first amendment, atheism has to be given the same status as a religion. It did not rule that atheism actually is a religion.