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Hmmm. Know where you're coming from, particularly about the fundamentalist atheist tendency - extremes create extremes and those wanting ANONYMOUS to go after one of the "big three" are, I would suggest, only interested in rationalism as a stick with which they can beat people over the head.
I think there's a subtle distinction to be made here between what Dawkins has said and what has been generally understood, and I don't think he has actually said that religion is the root of all evil, rather that 'evil' (however you may wish to define it, which is another subject entirely) tends to flourish where thought is based on half-truth or supposition as opposed to objective evidence. The title of his recent ish TV show The Root of all Evil was apparently not his choice and not one he was particularly happy with. Furthermore he has made very similar points to your own observation giving Martin Luther King and Johnny Cash as examples.
"Believing that "religion" is some kind of malignant non-material virus which causes problems in and of itself seems... superstitious..."
Not at all (although the malignance or benevolence probably is debatable), self-replicating ideas (memes) behave in an entirely viral manner. Apocalyptic cults (as an extreme example) tend to feed on insecurities so their beliefs are easily spread without any need for justification - that there really is a coming apocalypse, that the blind boy child can see again etc.
Personally, I'm uneasy with any one-size-fits-all philosophy, and I don't regard all forms of religion as being part of one great big nasty blob, but there's big grey areas here, and I'm distrustful of any belief sytem (whether religious or political) which facilitates censorship or other forms of oppression. I believe in the great majority of cases, religion can provide a convenient excuse without necessarily being the root cause, but I'm still glad we have Dawkins because I don't think hellfire preachers who believe homosexuals, non-believers, and people who teach the theory of evolution are "inherently evil" (for example) are just going to go away with a few hundred signatures on a petition.
"Religion, like any idea, is not a real thing but a way of explaining real things..." We both know this, but there's plenty who apparently think otherwise and are quite happy to express certain more extreme beliefs with unfortunate consequences.