As a "devout", heh, non-theist I feel that Midnight nailed it on the head with his first response. Is the regime a totalitarian repressive gov't or an "enlightened" scientifically advanced culture ala Vulcan (not sure if that is a good analogy as I am not that well versed in Trek culture, but I always felt that would be the case with Vulcans)
As a non-theist I am very accepting of others beliefs/faith as I was not born a non-theist I came to my non-belief through much experience and learning so it could be with an "enlightened" gov't. Then you could have state persecution of religion as there is persecution of believers of the wrong belief.
Basically you can generate an atheist gov't of any level of acceptance/oppression for your campaign. To make it believable, you just need to create the justification.
As a non-theist I am very accepting of others beliefs/faith as I was not born a non-theist I came to my non-belief through much experience and learning so it could be with an "enlightened" gov't. Then you could have state persecution of religion as there is persecution of believers of the wrong belief.
Basically you can generate an atheist gov't of any level of acceptance/oppression for your campaign. To make it believable, you just need to create the justification.