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The case that allegedly says "atheism is a religion" was brought by a prison inmate who wanted to have a separate study group set up for him and his friends who were atheists, and when the prison officials turned him down he sued claiming he was being discriminated against. The appellate court said:

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.”
[snip]
In keeping with this idea, the Court has adopted a broad definition of “religion” that includes nontheistic and atheistic beliefs, as well as theistic ones.
[snip]
Atheism is, among other things, a school of thought that takes a position on religion, the existence and importance of a supreme being, and a code of ethics. As such, we are satisfied that it qualifies as Kaufman’s religion for purposes of the First Amendment claims he is attempting to raise.

Source: here.

This is no big deal. Protecting the alleged sensitivity of a prisoner.