Why do atheists get singled out like this?

[Fred]

The main problem with religion at this point in our evolutionary thought is not the conflict between theist and nontheist as to whether a god exists or not...it is whether the rational will continue to allow the irrational to dictate the course of progress.

I think you hit it on the head here. It's deeper and far more pervasive than the existence of God question, at least as it plays out on the social terrain. Rational vs. non-rational is a major issue.

This is the ultimate end. There have been many points in history where this is easily clarified. There are of course recent events which make this glaringly obvious.

Can you list a few? I'd love to see what specifics you would point to because here's where I think it gets complicated.

Being politically correct is a detrement, toleration of any world view that seeks to harm others, suppress any form of rational thought, subjugate our species to nothing more than puppetry for the whims of unproven deities is ultimate genocide.

Your statement here has two different targets, the PC wing and the subjugation wing. If you can be said to represent the rational thought wing, and the fundies can be said to represent the irrational wing, where does the PC wing fit in? Are saying that it isn't a rational? Ok, but if it isn't, is it a different kind of irrationality? After all, if the fundie folk are seeking to subjugate and the PC folks are seeking to tolerate, that's two different brands right there, each coming from a different direction. What do you think that's about?

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A lot of Theists just cannot understand what atheism is.
We see this time and again here.

Heh. That "bald is not a hair color" bit just doesn't seem to be getting the job done, huh?

Theists say something to the effect "you dont believe in god, so what do you believe in?" when we answer "just not in god", it blows their minds,

I don't agree. They are perfectly capable of understanding that you don't believe in their God. The mind-blowing, or at least confusion, seems to come in the next step.

in their world you HAVE to believe in something, even if its not what they believe. But to not believe.....Just does not compute with them for some reason. Hence the fear.

To not believe in one thing is fine, but to posit the idea of not believing anything doesn't compute, because everybody believes in something. They believe in a world where deity is included, and you believe in a world where deity is not included.

To put it in the terms of that famous saw, they believe in a hairy world while yours is bald. They have no trouble understanding (even if they disagree) that you don't believe in hair, but to assert that you don't believe in bald, well, that doesn't compute and yet, that's what it so often sounds like what you are saying from their hairy pov.