The County of Lackawanna Transit System sells ad space on buses, but specifically excludes (among others) ads
that promote the existence or non-existence of a supreme deity, deities, being or beings; that address, promote, criticize or attack a religion or religions, religious beliefs or lack of religious beliefs; that directly quote or cite scriptures, religious text or texts involving religious beliefs or lack of religious beliefs; or are otherwise religious in nature.
Government-run bus systems can indeed exclude, for instance, all political ads, or implement other viewpoint-neutral restrictions; see Lehman v. City of Shaker Heights (1974). But the Supreme Court has held that an exclusion of speech that “primarily promotes or manifests a particular belie[f] in or about a deity or an ultimate reality” is viewpoint-based. Rosenberger v. Rector (1994). Such a restriction excludes religious (and anti-religious) viewpoints on various controversies — abortion, same-sex marriage, religious freedom, and more — while allowing secular viewpoints on such controversies.
So it looks like the Lackawanna policy is pretty clearly unconstitutional, and the plaintiffs in Northeastern Pennsylvania Freethought Society v. County of Lackawanna Transit System (M.D. Pa. filed Apr. 28, 2015) have a winner. On top of that, the plaintiffs — whose “Atheists. NEPAfreethought.org” ad was rejected — argue that the transit system “only began enforcing its policies after NEPA Freethought Society attempted to advertise with it,” which would itself pose a constitutional viewpoint-discrimination problem. See Cornelius v. NAACP Legal Defense & Ed. Fund (1985). But even without the argument that the system was hostile to atheists in particular, the facial challenge to the bus policy should succeed.