Madison expressly amends its antidiscrimination ordinance to cover atheists—who were almost certainly covered already
A Sunday AP story (Dana Ferguson) reports that, "In what is believed to be the first statute of its kind in the United States, Madison banned discrimination against the non-religious on April 1, giving them the same protections afforded to people based on their race, sexual orientation and religion, among other reasons." The amendment itself can be seen here; it changes the discrimination law (which covers housing, employment, public accommodations, and city facilities) to say "religion or nonreligion" instead of "religion."
It turns out, though, that discrimination against atheists is already generally treated as discrimination based on religion under such antidiscrimination statutes—and has been since the mid-1970s. See, e.g., Young v. Southwestern Savings & Loan Ass'n, 509 F.2d 140 (5th Cir. 1975); Cline v. Auto Body Shop, Inc., 614 N.W.2d 687 (Mich. Ct. App. 2000). It's fine to make this explicit, and may even be good (unless it leads more people to assume that other jurisdictions' provisions, which only say "religion," don't cover discrimination against the nonreligious). But it's nothing particularly noteworthy, either, given that this protection has long been understood as already existing under laws that simply cover discrimination based on "religion."
(I should note that not all laws treat the religious and the nonreligious identically; it's not clear whether laws providing special exemptions for religious objectors also extend to those who have secular philosophical objections. But bans on discrimination in employment, housing, public accommodations, and access to government services do indeed extend to discrimination against the nonreligious as well as to discrimination against the religious.)