I've repeatedly said the issue is not the religion per se - it is the underlying beliefs fomented, with or without religion:
Prejudice: 'our god is the real god, yours is false' - is extremely prejudicial and, however much a few religious people might fight it, this is an overwhelming product of religion. Which is also NOT to say that religion has exclusive access to creating prejudice.
Ideology: Ideology IS prejudice, human behavior is too complex to be fully captured by a set of rules. Any set of rules about human behavior is going to be harmful when the RULES themselves are placed above all else.
Tribalism/Us-versus-Them/Nationalism/Patriotism: These are more forms of prejudice - this is where religious and political ideologies both similarly exploit base human nature.
There is nothing wrong with a proportioned sense of pride about ones nation but no nation, government, or persons should be placed above open criticism. The point is that this "Us" mentality is highly exploitable and must be guarded against.
Credulity: that belief without evidence is greater than empirical facts and reasoned conclusions. 'God hates homosexuals, look here, he commands that you put them to death - we don't do that anymore but it is still an abomination - so no marriage for you'. No evidence of the harm this does to others can ever exceed the internally ridged inculcated mind holding that ignorance is greater than knowledge. See Also: Truthiness
Miracles/Supernatural: I don't have to take my child to the doctor, I'll just pray like it says in the Bible because I KNOW that miracles are real. There are many other harmful products of this belief as well (exploited by faith healers, psychics, and revivalists, .... just to name a few).
False Morals: the promulgation of poorly considered ethical foundations such as the Golden/Silver Rule (which only works if everyone agrees on the desired/undesired behaviors). Don't suffer a witch to live, stoning people to death, death for apostasy, genital mutilations, and so forth [varies]
The counters to these are skepticism, conservatism of action (in the sense of a proper sense of self-doubt as our condition is one primarily of ignorance), liberalism of thought (in the sense of throwing off prejudices, valuing education, freedom, and reform, openness to change in the face of new knowledge, guarding of civil liberties), and a scientific approach to knowledge that demands claims be supported by appropriate evidence and recognizes the propensity of the human mind for cognitive biases, illogic, and factual error.