The real criticism of religion's danger lies not with the crimes that have been committed in its name, but in its strength as a tool for social control. Any system which allows people to exploit others and excuse away deplorable acts is in some small measure a problem if people are allowed to abuse it unchecked (most systems of representative governance and organised religion are the two major examples, each of which has benefits to counterbalance the problems that they cause).
Please expand upon this. What specifically and plainly does religion do that is dangerous?
The biggest problem with this discussion is that no-one has defined their terms properly. "religion is dangerous" is an extremely vague and non-specific statement, as we haven't defined "religion" or "dangerous" (or even "is"). Still, it's worth answering anyway.
Religious beliefs by themselves do little - they are just ideas, not things. One might be able to argue that they can motivate or excuse actions, but ideologues are rare outside of radicalised social groups.
Organised religion, meaning the orthodox practices and methods of thinking of globe-spanning organisations with hierarchies, resources and other forms of social dominance mechanisms, are things and hence can be used dangerously (and may even act dangerously without conscious effort on anyone's part).
They are dangerous in the same way that a gun is dangerous. That is, they are a tool which can be used responsibly or irresponsibly; the responsibility for the actions committed is not with the religious meme or the gun as such, but on the people within the religion or the person wielding the gun.
That said it is becoming more and more difficult to seperate organisations from their constituent members. This is a matter of some debate in business academia. And we (that is, those in most civilised nations) also ban guns for a reason - the "benefits" that come from owning a gun are nebulous and are far outweighed by the potential problems. So realistically the answer is a complicated one and full of nuance.