The problem isn't with religion in itself, but with the idea that belief is a valid basis on which to guide your actions. Yes, most beliefs are harmless or even benign, but there is no difference in plausibility between the belief that you should be kind to others and the belief that anyone who doesn't share your religion can be killed as a righteous act.
That's what most atheists/agnostics are against - the authority of world-views that are inconsistent within themselves and observed reality, and that dismiss this inconsistency with the tenet that faith explains all. Since almost every religion (and pseudo-religious movement, like fascism or communism) shares this tenet, almost every religion is flawed in the exact same way, and is open to the exact same extremism.
You can't permanently solve that issue by replacing one faith with another. You can only solve it by discrediting faith itself.
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Better educated sadness than oblivious joy.
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