I agree that people often don't make the necessary distinction between ideas they have evidence against, and unevaluated ideas they've been ignoring because they've only heard them advocated by kooks. As you point out, only ideas in the prior category properly discredit their advocates.
Tyler Cowen argues in a TED talk (~15 min) that stories pervade our mental lives. He thinks they are a major source of cognitive biases and, on the margin, we should be more suspicious of them - especially simple stories. Here's an interesting quote about the meta-level: