Most successful religions are highly evangelical. This is how they become religious. They also have the view that their way of worship is the only and correct way to worship. Otherwise, people would not have to follow that religion. These two ideas, crucial to the spread of a religion, are not compatible with tolerance.

In fact, if you genuinely believed that worshipping a God in a specific way was necessary or you would face eternal punishment. Would you not want to save everyone else from this. The do not see it as intolerance. They genuinely think they are helping you. Others just see it as their tribe and have a use Vs them attitude.

For Atheists it is easier to accept and welcome others. There's no punishment for it. So tolerance comes easy. It's also necessary for religions to demonise Atheists, to control their flock. So the historical cultural perception of Atheists is not one of kindness and tolerance. That's why it's seems novel that reality doesn't match that.