No doubt atrocities have been committed both with religious and non-religious justifications. What makes religion the most dangerous of all is the most basic concept of religion - faith. Religion requires people to blindly believe in God and never question anything - if they ever do question, the answer is that God is much greater and mysterious and they shouldn't let their pride make them think that they know better, or something to that extend. This kind of thinking (actually this is the opposite of thinking) has been instilled for generations and people are inoculated from very early age.
The difference with other ideologies like fascism, communism, etc. is that they use fear as major means to control the people - the opposition to these ideologies was sent to concentration camps, gulags, etc. and the number of dissidents decreased very quickly - everyone stopped voicing their views when they saw how the most outspoken people disappeared. The majority of the population knew very well that the ideology was bullshit, but paid lip service to it out of fear. The moment the power grip was released, the ideology collapsed and the majority of the population overthrew the regime and never looked back. The differences with religion are obvious - no matter what the political, social, economical, etc. situation there is - religion is always there, always brainwashing, always on the prowl for the next wannabe martyr. You don't see many people saying that national socialism is good, just Hitler's interpretation was wrong, yet we hear this about religion all the time - Islam (or any other religion) is good, just the fanatics interpret it wrong...
Nationalism/patriotism is a bit different - similar to religion it is instilled from early age for many generations, so it can be used to manipulate people in a similar manner, but less efficiently - it works well when there is a significant threat to the country - people would give up their lives to defend it, but otherwise they would prefer to live peaceful and enjoyable life. Religion on the other hand can manipulate people in any condition - Bin Laden was a multimillionaire, he had everything you could think of, yet he still gave up his life (and destroyed the life of thousands) for an imaginary heaven.