Same thing happened to feminists. I was a feminist until they went crazy as hell and sued for things like lowering the standards to be a fireman. I'll be the first to admit that I would rather have a 200lb man made of solid muscle to carry me out of a burning building. Maybe the standards were lowered when firemen noticed that many Americans are simply too heavy to carry. Muscular or not, there ain't no way to carry a 300lb fatty on your shoulder.
I wonder how many people actually read the constitution or bill of rights (or the bible). In plain English it says the government shall make no law respecting an establishment of religion or prohibiting the free exercise thereof. The accepted interpretation is that this doesn't automatically keep the government out of all religious affairs, but merely prevents preferential treatment of one religion over another. Putting up a Christian memorial or a Jewish memorial should be totally acceptable as long as the government doesn't show unreasonable bias.
As a suitably apathetic atheist, I'm not as concerned with atheist representations being somewhat pretentious as I am with the same issues being had with feminism. Feminism has been a precedented, well-designed set of social conflict theories, since the term was coined. Even the whole "Third Wave" controversy was directed at its popular portrayals much more than its legitimate documentation, since newer feminist paradigms are just more comprehensive modernizations of older versions, IMO. I also suspect that "official" political representatives of feminism have been largely tainted by their corporate origins, if not somewhat deliberately (although I don't want to sound like a conspiracy nut, this is not uncommon as political deprecation tactic; most American political parties besides Democrats or Republicans have been affected by such things). Still, I have to give the present Anita Sarkeesian, Rebecca Watson, etc. era credit for being more subtle about their antithetically censorious implications than prior iterations of such things (just look at Jack Thompson; he was taken quite seriously, as a proponent of gaming bans, for quite some time, and he didn't even attempt to disguise his superficial, hardly even specious analyses of video games). Additionally, iconically ridiculous/hyper-offensive anti-feminist groups, most noticeably "men's rights movement", have been shown to make some pretty sneaky internet-based efforts to pose as feminists, often without directly serving to impugn them, as opposed to just influencing it surreptitiously (check out the recent "demmian" fiasco; this guy/girl RUNS the presumably official/primary Feminism subreddit, and he/she has been pretty substantively suspected of being an MRA, having stated some pretty adroit, ostensibly innocuous commentaries about hypothetically merging feminism and "men's rights", despite established intersectionality calling this into question, AS WELL AS being a co-moderator for a reddit directed at pedophiles, though I think it's still unclear why exactly he was doing that, or what his/her rebuttals are, if any exist.)
EDIT: the thing with demmian has been made much more obvious, since I last checked. His banning habits strongly favor MRAs over feminists (I was incredulous about this, since I was banned a while back for being genuinely and deliberately obnoxious, though very much a feminist), and most now recognize this deal for what it is.