I realize I'm not the best one to answer this question. I know I have some Republican readers, so maybe they'll chime in. But I'll try to offer some suggestions at least to get the discussion going.
I suspect one will find a minority within almost any population that will appear to vote against their self-interest. The reader who raised the question of atheist Republicans compared an atheist voting Republican with a Black person voting for David Duke (former Klan leader). I understand the comparison, but I suspect there were at least a handful of Blacks who did in fact support Duke. From what I've seen of atheists, the vast majority tend to be on the liberal side of the political spectrum. But there will inevitably be some who do not.
I would guess that most atheists who support Republican candidates do so because of their fiscal policy and not their social conservatism. I realize that it is increasingly difficult today to find a Republican who is not rapidly anti-secular, but this hasn't always been the case. Perhaps some Republican atheists simply try to work around the worst offenders among their candidate pool because they agree with the economic side of the platform.
I suspect that other atheists vote Republican because they agree with the Republicans stance on defense, gun rights, and other policy issues. Perhaps they view these issues as being so important that they are willing to overlook the fundamentalist Christianity embraced by much of the Republican Party.
Consider members of the LGBT community who vote Republican. Perhaps they have no interest in marriage, are fine with civil unions, and agree with most of the rest of what Republicans stand for. I know, I have a hard time wrapping my head around it too. But I can at least imagine how it might work.
I suppose the question for any atheist Republicans reading this would be something like this:
What is it about the Republican Party that appeals to you so much that you are willing to disregard their stance on church-state separation and other concerns common to atheists?But you know what, I think the same question could fairly be posed to those who support today's Democratic Party. Could that not be part of what we are seeing here? People support anti-atheist candidates because that is almost all we have.
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