I think Sam Harris made that point about religious moderates, although he was talking about Islam: the moderates provide cover for the fundamentalists and represent a halfway house between secularism (atheistic naturalism, liberalism, etc), and archaic religiosity. There's some logic to saying that, but I'm not sure it supports the claim that moderates are worse than religious extremists. Practically by definition, moderates are semi-modernized or secularized, so they're closer to atheism than are the fundamentalists. An atheist should therefore have a hard time treating them as the fundamentalist's equal.

I'd reframe the criticism by saying that moderates present a unique challenge for atheists since the moderates cling to an empty shell.