The Paradox of tolerance doesn't mean what you think it does. It talks about "unlimited tolerance" which already doesn't exist under law or the first amendment. We have many restrictions on freedom of speech, such as incitements to violence.

The author also states explicitly that his words shouldn't be used to "suppress the utterance of intolerant philosophies; as long as we can counter them by rational argument" and that such extreme action should be reserved for situations where all else has failed and we're up against "fists or pistols"

Violence, not words, is the problem. Thankfully we're not tolerating their violence.