Most people who advocate tolerance are caught in a paradox. They believe in tolerance, but they feel helpless against intolerance. It seems hypocrisy to be intolerant of intolerant behavior. This article from Stand to Reason has a good solution: When tolerance is intolerance.
Quoting Peter Kreeft, the proper understanding of the paradox should be:
“Be egalitarian regarding persons.”
“Be elitist regarding ideas.”
Simply put, we continue to exhibit tolerant behavior by being civil to one another. Even with intolerant people, there are proper ways to put them in their place. However, we have to be intolerant with harmful ideas like intolerance or racism. Using tolerant manners, we combat them properly so that Reason prevails.