Now, if you read the list here, there are things in it that I can see as valid points of disagreement.  But this…well, I’ll say this for these guys, they really do know how to sum up the insanity, fear, and hatred or the rightwing conservative movement. 
Again, in just one line, the get at a fundamental conflict:
Intellectual Conservative Politics and Philosophy

He said, “*You need to make sure your child can speak Spanish” and that it’s “OK to provide government services in Spanish.” He also “voted NO on declaring English as the official language of the US government.”

These guys have actually caught my eye more than once on a number of topics (like how the people in New Orleans should be grateful that they got any help at all,
regardless of how toxic the trailers are), but this one is particularly sad, and seen too often:

Intellectual Conservative Politics and Philosophy

FFRF is wrong when they claim that religion is responsible for the worst events in history. There has been more bloodshed under the name of atheism than under the worst Christian hypocrites. There are several recent examples. Hitler called Christianity a disease and predicted he would see its demise. Under the Third Reich, 11 million people were slaughtered. Karl Marx started communism based on an atheist philosophy. Stalin and Mao Tse Tsung adopted Marx’s communist rule, killing tens of millions. Under the atheist Pol Pot regime, around 2 million lost their lives, about one quarter of the population of Cambodia.

So, we’ll start with the factual inaccuracies first.
Hitler, while not a christian, was NOT an atheist.  A review of his speeches and other sources proves this beyond doubt.
As far as Stalin goes, while it is very clear that he felt religion would get in the way of his rise to power, that does not imply he is an atheist.  How many people do YOU know
who claim to be of one religion or another until it is inconvenient for them?  Does every jew keep kosher?  Does every Christian go to church every Sunday?  Does that make them
atheists?
Further, the logic of the statement is certainly more dangerous to religious people than atheists.
Basically, Ms. Alexander is comparing the atrocities these men committed to be comparable to, say, the Crusades or other jihads.  If they are, then religion and atheism are equal in their potentially destructive nature.  The veracity of the conclusion is irrelevant, because the comparison doesn’t support the claim.
The Crusades were motivated by religion, without doubt.  But there is no reason to think that Hitler and Stalin were motivated by atheism in their regimes.  So, what Ms. Alexander is actually saying is: If an atheist does something horrible, then atheism is playing a crucial part, and atheism can take the blame.
That would be fine, I suppose, but I doubt that she’d like to extrapolate from there, because the same would have to be true for religious beliefs as well.
Any time a christian did something bad, we’d have to blame christianity.  Or whatever religion. 
Since the vast majority of world leaders have been religious people, and, actually, the vast majority of people in general have been religious (at least in the western world), then virtually all bad-things can be attributed to religion.
According to Ms. Alexander’s logic.

“Intellectual” indeed.