Fundamentalists of any stripe are scary in some sense. But fundamentalist atheists are mostly just annoying, because mostly they don't believe their beliefs should be enforced by the state.

Its the relationship between church and state that is the worry, not the metaphysics. Islam used to be tolerant in the middle ages, because they believed in a (somewhat) pluralist state (at least by the standards of the time), now the Islamist concept of the relationship between church and state is all screwed up.