The Normans captured Pope Leo IX in 1053.
Soviet Russian troops overran many nations.
North Vietnam's Viet Cong won over South Vietnam and the US military.
Religious adherence is no guarantee of victory against secular troops.
That being said, in my four years in the USAF I saw no religious discrimination against atheists or agnostics or any other religion (other than in basic training where Christians got to go to church on Sunday and everybody else had to clean the barracks).
Atheists are America's most despised religious minority, yet they are overrepresented in the US military, and underrepresented in the prison system; and not known for flying planes into skyscrapers.
In addition to Christians being permitted to attend church on Sunday, the military chaplaincy also saw to it that Jews & other SD types were free on Saturdays and Muslims on Fridays.
The whole point of recognizing religious requirements is that one make decisions to accomodate that requirement. If one (an atheist, for example) has zero requirements, then it’s hardly fair to criticize the system for not accomodating that which doesn’t exist.
I don’t think atheists are the most despised religious minority. First, they claim not to be religious at all. Second, most outrageous cults are far more despised.
Since atheists have no practices, identifying marks, requirements, etc., they really are simply out of sight.