Atheists and Secular Humanists are protected by the First Amendment regardless of whether their belief systems are "religions" or not
A recent federal district court decision holding that Secular Humanist prisoners are entitled to organize a discussion groups focused on their beliefs on the same terms as theistic prisoners is easily misunderstood as relying on the conclusion that Secular Humanism is a religion. The judge did indeed note in his ruling that "[t]he court finds that Secular Humanism is a religion for Establishment Clause purposes." However, at another point in the decision, he also wrote that "the touchstone of the Establishment Clause was 'the principle that the First Amendment mandates government neutrality between religion and religion, and between religion and nonreligion.'[McCreary County v. ACLU], 545 U.S. 844, 860 (2005) (emphasis added). Thus, whether Humanism is a religion or a nonreligion, the Establishment Clause applies." Just as the Establishment Clause protects Christian or Muslim prisoners who wish to hold a discussion group where they promote belief in God, so it also protects Secular Humanists or atheists who want to promote the opposite view.
From an Establishment Clause standpoint, it does not matter whether Secular Humanism is a "religion" in any deep philosophical sense, but only that it entails beliefs about religion. The key question is not whether Secular Humanism is a religion, but whether equal treatment of Secular Humanists is a component of nondiscrimination on the basis of religious belief. The answer to that latter question is yes. Even if Secular Humanism is not a religion, it clearly entails rejection of commonly accepted religious commitments (such as belief in various gods and other supernatural forces). Discriminatory treatment of people who reject these types of religious beliefs is discrimination on the basis of religion in much the same way as discrimination against people who refuse to support any political party or ideology is discrimination on the basis of political belief. As the district court decision points out, Supreme Court precedent has long held that the Establishment Clause forbids discrimination in favor of religion against irreligion, as well as in favor of one religion over others.
The Supreme Court briefly referred to Secular Humanism as a religion "which [does] not teach what would generally be considered a belief in the existence of God" in the 1961 case of Torcaso v. Watkins. But, as in the recent district court case, the result in Torcaso did not depend on whether Secular Humanism qualifies as a religion or not. As Justice Hugo Black put it in his opinion for the Court, "We repeat and again reaffirm that neither a State nor the Federal Government can constitutionally force a person 'to profess a belief or disbelief in any religion.' Neither can constitutionally pass laws or impose requirements which aid all religions as against nonbelievers, and neither can aid those religions based on a belief in the existence of God as against those religions founded on different beliefs." Thus, it makes no difference whether a law discriminating in favor of theists against atheists or secular humanists qualifies as favoring religion over non-religion or favoring one religion over others.
Some of the previous coverage of the district court decision seems to conflate Secular Humanism and atheism. In reality, many, perhaps most, atheists do not consider themselves to be Secular Humanists (myself included). And a few self-described Secular Humanists are theists. Atheism is simply rejection of the existence of deities, and is potentially compatible with a wide range of different views on moral issues. Secular Humanism has many variants, but is usually interpreted as a broader ethical theory that includes components that go beyond taking a position on the existence or nonexistence of deities.
Be that as it may, the same legal principles that protect Secular Humanists and conventional religious believers also protect atheists. In my view, atheism is not a religion in the conventional sense of the word. I think this is also true of most, though possibly not all, variants of Secular Humanism. But, as far as the Establishment Clause of the First Amendment is concerned, it does not matter whether atheism, Secular Humanism, or any other belief system that takes positions on religious issues is actually a "religion" or not. People who reject religion, or are simply indifferent to it, can still be discriminated on the basis of their beliefs about religious questions or lack thereof.
Things are perhaps more complicated under the Free Exercise Clause of the First Amendment than under the Establishment Clause, since the former protects the "free exercise" of "religion," which suggests that the free exercise of secular beliefs can still be restricted. But, at the very least, free exercise of religion still entails a right to reject religious beliefs and urge others to do the same. Thus, the Free Exercise Clause surely at least encompasses protection for the free exercise of secular beliefs about religious issues, even if it does not protect secular views of morality more generally. As prominent First Amendment scholar Doug Laycock puts it, "the Religion Clauses [of the Amendment] should protect freedom of belief about religion, not just beliefs in religion."