I would say the issue at hand is very much religion or non religion. I take tolerance to be a given; we're all civilised people, after all.
The problem with a lot of religious people is that they seem to think that when someone says they don't believe in the whole concept of god and religion, they are actually saying that they believe/ are sure that god doesn't exist, and then go on to assume that the two positions are equivalent.
For instance, I am quite satisfied with the explanation that science currently provides for the situation we are in. Their theories seem reasonable, they have loads of data to back them up, they make predictions based on their theories, conduct experiments and the results corroborate the theory. This seems like a reliable method of enquiry and I think it's reasonable to base one's view of the world on these theories. The idea of god is not needed at any point to explain anything; it doesn't contribute anything to the proceedings.
Religion, on the other hand, only has a few texts written by a couple of guys at a time when people didn't understand half as much about the natural world as we do now. It posits the existence of an entity that doesn't really explain anything, it just raises more questions.
Since this religious theory doesn't contribute anything to my understanding of the world, I feel justified in discarding it for now. I'm always able to come back to it later, if I'm presented with evidence that points strongly in its direction and for which no other reasonable explanation can be given.
This is because science is an open system; things are provisionally 'true', until a better theory comes along, one that does a better job at explaining the phenomena.
Religion, by contrast, is a closed system. It asks you to accept its theory for now and ever after, and never mind evidence, because 'that's not what religion is about.' In my view, this is not a reliable way to come to an understanding of the world.