Religion is just any arbitrary set of beliefs. You cannot be tolerant of all arbitrary sets of belief and expect to get any sort of stability out of it.
That's taking the concept to an absurd extreme. Totalitarian belief systems that can't coexist with others can't be tolerated, yes, but it's nothing inherent in christianity - yet different Christian denominations spent decades killing each other in the Thirty Years' War. It's more of a character trait. Same personality type that was happy to kill all 'papists' would be a fanatic nazi in 30s' Germany and an eager killer for Pol Pot.
People like that are always going to exist, what happens depends on the reactions of the other members of the same 'tribe'. If they oppose it nothing happens, if they ignore it or, worse, weakly support it, the situation deteriorates in a feedback loop until both sides convince themselves that everyone from the 'enemy' camp wants to kill them, so the only option is to kill them first.
You're the one who made the claim. If your idea can't handle the "absurd extremes" then your idea is wrong. Frankly, religious beliefs that include intolerance of other religious beliefs are empirically the rule, rather than the exception, and you don't need to be a mathematician to figure out how that throws a wrench in your characterization.
Well they are not arbitrary, and they are deeply historical and have tons of context. Even if you cite the church of the flying spaghetti monster, well it has exactly 0 followers. Also in the countries where there is still violence due to religion (ie. ISIS conditions) but made speech 100% free (or free as in US style rule) it is very likely the violent elements will mostly go away. That's assuming you "could" - in most of these countries it's a long way off.
Forgive me if I am misunderstanding your statement - "Even if you cite the church of the flying spaghetti monster, well it has exactly 0 followers."
Our faith has many followers. Also, among religious communities, we are shown to put our money where our mouth is. We back our beliefs, as do other faiths, with charity/cash.
I am happy to be part of a religious congregation that, in the context of microfinance/lending to strangers (not for profit, by the way), performs admirably when compared with more popular, mainstream religions:
But can I ask you, do you actually believe the FSM exists or is it more of a statement about how nutty religion can be? Because that's what Wikipedia says, not a religion, a social movement.
"is a social movement that promotes a light-hearted view of religion and opposes the teaching of intelligent design and creationism in public schools"
