The problem with the "Paradox of Tolerance" is that intolerance of the "intolerant" drive the "intolerant" underground. They may feel isolated for long periods of time, but when they realize that they are the majority, rather than the minority, power can shift dramatically. This is called a "preference cascade" and it's particularly common among totalitarian regimes.
The only way to prevent preference cascades is to have just enough tolerance of views you consider hateful that they don't get driven underground -- and you do this by rigorously debating anyone you find to be wrong, without going after their livelihoods (among other things).