It's less about tolerance of people and more about tolerance of beliefs, but more importantly actions. It requires personal agency and bodily autonomy to be sacrosanct to function. Ergo, if you wish to cut off your arm and make a taco out of it, that's fine, but you cannot force someone to eat said taco, nor can you force someone to assist you in cutting off your arm. It's your body, your choice, your action, and your consequences.

This means, if you have a religion where women are viewed as inferiors, that's perfectly fine to have. You can believe that women are lesser beings as much as you want, and you're free to treat women like the complete and total dickwad you are, but you cannot violate their personal autonomy. You cannot force anyone to partake in your beliefs or act in accordance with your beliefs.

I'd say that roaming gangs of people harrassing others does impeach on said others' personal autonomy, and thus wouldn't be tolerated.

Believe that homosexuality is a sin? Great. Don't engage in homosexuality. Believe that your labia needs cutting off? Great, do it, find someone else who shares your belief and have it done to you. You may not force this upon your daughter though, your rights end where hers begin.

You're allowed to have your god, and someone else can have theirs, even if said gods are complete polar opposites and clash with one another. Deal with it, or sod off.

Then you'll have to take it on a case by case basis. Like with everything. There's no perfect system. There never will be a perfect system.