A very classical issue that occure not only in RF but in daily life on earth, is that people judge everyone from a group if one of them do wrong.
Example if one muslim do wrong, every muslim must be evil.
If one Christian do wrong Christianity must be evil?
How about if a car mechanic do an evil action, example murder or rape, does every car mechanics become evil human beings?
So why Do you judge differently if a bad person come from a religious background?
There is quite a huge difference between the comparisons you make. Being a car mechanic is an educational profession and tell you nothing about a person. You can be a muslim, atheist or christian and a car mechanic at the same time.
However it is not possible to be an atheist and muslim at the same time. Obvious reason being that these are labels that describe a person's view on religious matters.
And with each label comes a lifetime of personal experiences and teachings, sometimes these views are taught to people from the very beginning of their lives and in other cases they are arrived at. But where a car mechanic is taught how to fix cars, a person brought up with or without religion is taught how to view other people, the world and the society to which they belong. What is right and what is wrong. What and how people should and shouldn't be punished based on their beliefs.
Religions have many path, not all Christians agree with all other Christians and not all Muslims agree or are taught the same as other Muslims. But equal for all religions is that they teach people what others before them believe to be true and just, based on traditions and interpretations, rather than facing the hard questions themselves of what is actually most likely to be true and just.
It just happens that some religious teachers within these religions prefer teaching unity and to some degree acceptance of other religious or non religious views, more than others do. But in the end they all follow the formula as those that encourage hate and non acceptance of other views than their own. Something based on personal interpretations of old texts rather than what life itself throws at them.
Certain things are taught to religious people, whether they like it or not, like there being only one true version of God and that it is their version, if they did not believe that, they wouldn't follow that religion. And since lots of cruelty can come from these texts depending on how they are interpreted and taught to others, which only belong to that particular group of religious people. Then it is fair to say that certain things spring from certain religions and not others. Meaning, that you would never find an atheist judging other people based on what is written in the Quran or the bible as if they were an authority on what is right and wrong. Just as you wouldn't find a muslim using the Christian bible as such either.
So just as people will judge atheists for their non belief, so will we judge each other for having chosen the wrong religion or one at all. But as we know, that doesn't mean that we for the most case, find all of a certain view to be wrong or evil. Simply that their wrong beliefs or lack there off in certain cases give them the possibility of holding certain views or do things that do not make sense in our world view. And you will find that even within people of same religion, Islamic terrorists will still harm those of the same religion, because to them, they are not true muslims. Their interpretations and former teachings are not inline with what you might believe true Islam is. But as I said, the method used to arrived at these teachings are the same, it's others personal opinions and interpretation of old texts, taught to others as if they were true, with little connection to life and reason itself, if you ask me.
I can only speak as an atheist myself, but I judge all religions the same. Im simply happy that most of the teachings and interpretations seems to prefer unity and acceptance of others rather than not.