I find that a rather odd question since it puts them on a level of equal validity.
I don't know of any militant atheists that are calling for science or "atheism" to be taught in churches at taxpayer expense. Laws aren't based on "atheist" statements, unless one equates math, statistics, etc. as strictly atheist. About the most militant way I can think of atheism being put forth in law is some that are demanding the tax-exempt status of churches be revoked.
So if someone wants to make birth control harder to get, make discrimination against minorities easier, or codify deities into state laws/practices because they say a god demands it, then those people are more annoying, since they're a real-world detriment to everyone that doesn't believe as they do.