I think you're glossing over some valid arguments that aren't based on double standards:
- training people to accept beliefs or follow authority uncritically - even if the beliefs they're being trained with are benign in and of themselves - can make them vulnerable to being misled by people who present them with harmful beliefs.
Harmful beliefs can just as easily be the result of logic, evidence and reason. We make decisions based on bounded rationality which frequently leads to the wrong result.
I'm a bit sceptical of this idea, and think it would be pretty difficult to demonstrate its validity scientifically due to the difficulties in isolating variables.
when a person proclaims that they uphold a creed that justified violence or harmful acts in the past, they take on that legacy of violence and harm. I can't take someone seriously who tells me that he believes that the entire Bible was inspired by God and then turns around and says that his beliefs have nothing to do with people who took parts of the Bible like "do not suffer a witch to live" seriously. OTOH, atheism has no creed; the creeds of individual atheists vary, and the creed of a modern skeptic, freethinking, secular humanist is not the same creed as Stalin, Pol Pot, or any of the other nasty atheists who theists like to trot out when they feel threatened.
Atheism is a belief not an ideology though. It isn't a valid comparison really.
Almost all major ideologies carry around significant amounts of baggage. Do those who advocate democracy and human rights have to accept the Iraq War on their conscience even if they bitterly opposed it?
Why should a 21st C Quaker pacifist have to carry the entire history of Christianity on their shoulders?
Religions can be used to mean pretty much whatever you want them to mean.
They support such a wide range of interpretation that there is no real value in considering any of them a unified ideology. Considering things which happened in a different time, context and place as part of the same ideology is even more meaningless.
Witch hunts have existed in all societies, and practitioners of black magic are still being killed today. This isn't necessarily because 'god told me to kill them', but because people believe in magic and its harmful effects.
As a someone who is not religious, I don't feel responsible for communism. I also don't feel that a modern Christian should feel responsible for what happened in the 11th C either. Religious believers can and should be criticised if they support or condone immoral acts, but when they don't they shouldn't be held accountable for alternative interpretations.
If someone wishes to generalise though and criticise others for beliefs they don't hold and thoroughly condemn just because they are nominally 'Christian' or 'Islamic', then they can't pretend that a flip side to this line of reasoning is equally legitimate.