If you stop treating it as a moral commandment and instead consider it a treaty which allows civilization to exist, it becomes obvious that it doesn't apply to those who won't remain bound by it. It's not a paradox.
Tolerance is for all points of view that will allow the discussion to continue.
I trace tolerance in general back to the religious tolerance introduced by the Peace of Westphalia, and the centuries of religious war that preceded it. It obviously goes much further back, but that's the archetypical example for me.
Seen in this light, tolerance is somewhere between symbiosis and mutually assured destruction, and much less wishy-washy than everyone thinks it is.
Tolerance is for all points of view that will allow the discussion to continue.