They (non-religious) may not express their intolerance with violence, but they express it with repression, fear and paranoia. With suppression and segregation.
ISIS are killing christians, but my point is that they are killing Shia. These are muslims. The issue is not one of religion. It's an issue of politics. The shia and sunni in the area ISIS is controlling have been tribes at odds, one repressing the other for political reasons.
This needs to be fully understood before putting the blame on religion.
I mostly agree with your point and in basics the religions are not the reasons for wars/fights/killing/slaugtherings, but you can see them as tools!
It sounds negative, but human beings always have used tools to rule other human beings and in the past religions have been setup to rule over 'their' people!