I don't think religion is 'the root of all evil' - the dangers and direct negative consequences have been somewhat exaggerated - nor do I think being religious is devoid of (non-epistemic) value. However, the ultimate source of religion is responsible for much human suffering, both religious and secular. The suppression of science and reasoned debate, numerous wars, Islamic terrorism, the atrocities of Torquemada, Nazism, intolerance of various kinds (xenophobia, homophobia, the persecution of atheists, etc), Communism, Objectivism, cultism, quackery, silly public policy, and many others have numerous causes, of course, but perhaps the most important is unreason and insensitivity to evidence. The cradle of most people's religious beliefs - credulity, dogma, obscurantism, faith, insufficient humility in the face of the complexities of the universe, close-mindedness, an uncritical acceptance of what you happen to have been exposed to as a child and other vices - is also one of the principal causes of the evils listed above. The single most malignant feature of religion, then, is that it celebrates and defends an unjustified epistemology (roughly, how to know) that is also the source of, and can thus lead to, innumerable types of evil. As Voltaire put it, "those who can make you believe absurdities, can make you commit atrocities".
(This post was inspired, by the way, by Greta Christina's daily 'atheist memes' on Facebook).