I read the first post carefully and the next few posts quickly, but not the entire thread, yet.
I am a pretty radical thinker and this topic is a big, radical idea, which I find interesting but adamantly disagree with. I have recently developed more anti-tolerant views of religion, especially as it interferes with the progression of humanity in some ways and the resolution of important issues that affects everyone, not just the believers of a certain religion. I don't think religion has any place in politics or big decisions. I won't go as far as condemning religion as a social practice and eliminating the entire group to radically change the status quo and the way everything works.
And this is why: We will all disagree with one another at one point or another. Just because a majority believes one idea doesn't mean the four groups of minorities are wrong. This is the danger. It is presumptuous to think that the majority will always be logical or that the group of extremely intelligent, logical and innovative people will be the majority. That's the problem. It is seemingly progressive and unproblematic if the group who is Right gets to eliminate the group who is Wrong, but who is the judge of right and wrong?
Civilization does not belong to one group or one person or one idea, it belongs to all of us. How we will progress belongs to ALL of us, the strong, the weak, the average, the religious, the anti-religious, the short and the tall. It is not logical to wipe out the opponent because there will Always be opponents to wipe out. If there is one threat to civilization, then sure, eliminate it for a stable, peaceful and radically different future. But there isn't just one threat, the number of different ideas and people is immeasurable. If we all stick to one idea because all other ideas have been removed by force, we actually will also reach a stagnant without fresh batches of ideas, even threatening, competing, completely insane new ideas.
Life means something different to each person; it doesn't necessarily have to be logical to be a legitimate perspective. We are not robots. We differ tremendously by principles. If we don't tolerate each other, we will all end up killed by another group/idea ... eventually. No one can be the ever lasting winner if we refuse to tolerate. Unless we stop thinking of new ideas, which is pretty disturbing in itself and obviously not good for humanity anyway.
That's my general perspective on why tolerance is important; it's for everyone's safety. But nothing is 'always' the best solution.