Considering someone mindless might be rational, hating him for it is not. Atheists (also represented by nazis and communists, who replaced God with an idea of "collective good") might be just as militant as their religious neighbours. The point is, that you cannot judge person by ideology he was brought up in.
The core difference is that those that are religious and are brought up to believe in a mono-theistic god, and currently still believe in their faith(Or self-assign themselves as (x) i.e Muslim, Christian, etc),
must believe in their holybooks as well, of which promotes violence, murder, rape, hate, etc. Being selective is not an option when it comes to theists, or they are not theists anymore.
While an atheist is not self aligned to any such medium. There is no book that they follow.
That is why some people such as those in "Terrorist" groups like ISIS, etc, use their holybooks to justify their actions, because their actions are indeed promoted in their books by their "god" and "prophets".