1. Isolationism works in the Marvel universe. Most of it's advanced societies are small isolated populations. Examples include Wakanda, Latveria and Attilan.
2. The Government is sinister and doesn't have the common mans interest in mind. Examples Virtually every mutant story ever told involves extremely well funded government organizations, that are more then willing to
a. experiment on it's own citizens.
b. murder large numbers of said citizens, either deliberately or indirectly.
This combined with the shear number of politicians that are shown to be corrupt or down right evil, paints a picture of the government(US in particular but not exclusively) as a sinister entity.
3. True atheism is an impossibility. Their is no way an average citizen in the Marvel universe could see the stuff they see routinely, and not have some level of theism. The Average person in Marvel New York has probably seen aliens, gods Lovecraftian horrors, and even magic,and a bunch of stuff that doesn't obey any of the laws of physics as they would understand it. Agnostics, yes, probably a bunch, but outright atheists, highly unlikely.