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A few years ago, DJ Grothe (host of the Point of Inquiry podcast) and Austin Dacey, both of the Center for Inquiry, wrote an article in Free Inquiry magazine (got all that straight?) that has re-emerged among science/atheist bloggers recently.
Grothe and Dacey argued that atheism was not a civil rights issue.

… is it really legitimate to compare the situation of nontheists in America to the oppression of women, ethnic and racialized minorities, and the GLBT community? Can their struggle for public respect be modeled on the civil rights struggles of the last century? In fact, the analogy with gay rights is seriously flawed. Atheists need a public awareness campaign, not a liberation movement.

Atheists are not denied equal access to housing for lacking belief in god, nor are they kept from seeing their partners during life-threatening scenarios in hospitals. Atheists don’t earn sixty-five cents for every dollar earned by believers, nor are they prevented from voting.

They had a good point. They went on to say that atheists were also not physically beaten as many other minorities have been (though, truth be told, we’ve seen cases where that has happened). Also, they added, the fact that we can’t get elected as president is not a civil rights issue– it’s an image issue.
Eddie Tabash, a California attorney, disagreed and wrote a piece for the same magazine. So did Margaret Downey, current president of Atheist Alliance International. After citing examples of how atheists were treated as second-class citizens, she said this:

One would think that any atheist who had experienced discrimination would be eager to submit an affidavit [for the purpose of a lawsuit]. Instead, the fear of suffering further discrimination as a “whistleblower” was widespread. Some victims told me that they did not want to go public lest still more hatred come their way. This is the trauma of discrimination, just the sort of intimidation that discourages discrimination reports and makes it difficult to find plaintiffs for needed litigation.

Had Grothe and Dacey contacted me before writing their article, I could have opened my files and shared accounts of physical and mental abuse, job loss, cruel media stereotyping, and other instances of discrimination. I believe they would have been satisfied that “atheist bashing” really exists and is getting worse.

There was also a rebuttal (PDF) to the rebuttals.
In fact there are many cases of blatant and not-so-blatant discrimination against non-religious people.
Back to present day.
Matt Nisbet recently reiterated the notion that atheism is not a civil rights issue and all hell broke loose.
PZ jumped in the fray and said they were all wrong and it is a civil rights issue:

[Grothe is] resting his argument on the fact that atheists haven’t suffered comparable harm to minorities and women, and yes, we already know this. We aren’t being lynched or imprisoned in our own homes, we’re just being metaphorically kicked in the shins every day. The fact that injustices are small does not change the fact that they are injustices, nor does the fact that there are greater crimes being committed mean that the littler ones should be ignored. Grothe’s litany of greater problems is nothing but a demand for passivity from atheists.

Jason agrees:

The question isn’t whether there are groups in American society who have greater reason than atheists to feel aggrieved. The issue is simply whether atheists have anything to learn from the struggles for acceptance of those other groups. The answer, it seems to me, is an obvious yes. In each of those cases a despised minority was able, over a period of many years, to attain a position in society of far greater visibility and equality. Atheists also face a situation where open hostility towards them is considered acceptable, and in many parts of the country face outright bigotry when their views become known.

He adds that our PR problems are not coming from the likes of Sam Harris and Richard Dawkins who may come across as unpleasant to many religious people. They are coming from the religious bigotry and ignorance that is so rampant when it comes to perceptions of atheists.
Grothe is now responding to the comments:

… speaking strategically, we should also just admit that our moral indignation, our anger, is not on par with those who marched on Washington in 1963 to end public school segregation, and for legal protection against police brutality, and to make it illegal to racially discriminate in public and private hiring, and the like. Our indignation is not about how oppressed we are in society, but about how wrong we think society is to believe destructive nonsense. Even so, many atheist activists have put the beleaguered atheists’ plight on par with sexual or racial minorities. The same goes for many Christian activists who are these days talking about Christians themselves being the last oppressed minority in America. Both are wrong. Being popular is not a civil right.

Grothe adds another comment here.
One person has already said Nisbet would have a different view of atheist discrimination if he didn’t live in Washington, D.C.
No doubt there are atheists who have lost jobs as well as friends because of their religious views. Just because the laws aren’t in the books, there is still de facto discrimination. While it’s not nearly as horrible as what other minorities have had to go through, it was through conscious-raising on their parts that they became more accepted. By bringing light to how atheists are treated in this country, and how many churches and well-meaning Christians are in large part to blame for that, that’s the only way we are going to be able to make a positive change happen.

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