I'm neither tolerant nor intolerant of what religion people have, just like I don't care how they go about brushing their teeth. You wanna say a turtle made the world and you must always wear a hat, and that this is an undeniable truth and law if the universe? Great. So long as the government and society doesn't give special preference to that idea vs, say, flat-Earthers or geocentrists, everything's fine.
You are fine if they do things "over there" but as soon as it has anything to do with you you are intolerant.
Everyone is like that - even people who call themself intolerant. You call yourself tolerant, but when push comes to shove you are actually not.
You should stop lying to yourself and actually look at your own thought process to at least be aware of it, even if you are unwilling (or unable) to change it.
To say you "tolerate" something implies you're against it, but you're gonna allow it to go on. Should I say I "tolerate" Justin Bieber? That'd be pretty arrogant of me to say. As much as I dislike his antics, I, as some random member of the public, should not be able to be in a position where I can be intolerant of him.
An enhanced focus on rationality, critical thinking, skepticism, rejection of magical thinking -- all these things will build inoculation against these particular shitty ideas.
Unfortunately, that also means dismissing religion, deriding modern politics, etc. But as a first start, getting rid of "freedom of religion", and instead focusing on freedom of {speech, expression, association, gathering, thought} wouldn't be bad. It'd cause people to think a bit more critically of what they mean by freedom of religion and so on.