The answer I'm tempted to give is "Yes. It's right in the name."
Serious answer: "You can't tolerate intolerance" is a stock phrase used in multiple contexts with different meanings, some of which I think are justified and some I think are not. Sometimes it's used in response to whining about how "Christians are the only group you're allowed to persecute" in response to a story about legalising gay marriage, or equivalent. Sometimes it's used to justify any manner of action against someone who isn't deemed progressive enough.
My main objection is that "You can't tolerate intolerance" is stupidly phrased, because it combines two different meanings of the word "tolerance" and essentially says one of them is always good and the other is occasionally bad. "Tolerance is great, and therefore intolerance sucks!" and "when something is horrible, you cannot tolerate it!" are both applying valid meanings of the word "tolerance", but they are necessarily different meanings. It's not a good idea to use them in the same sentence without further clarification.
When I say we should tolerate intolerance, I mean, specifically: "Tolerance as in the idea of being able to coexist with people even when strongly dislike them for whatever reason is important. Some people will not appreciate the importance of that, and it's justified to dislike them. It's justified to argue against them, to criticise them, to mock them, to think they are stupid. But when the very idea of someone who is intolerant offends you so much that you think that anything is justified against them, you have failed the very principle you are defending".
And sure, the line where action goes from justified to unjustified is blurry and hard to determine (as pretty much every ethical question is). Phrases like "you can't tolerate intolerance" or "freedom of speech is not freedom from consequences" don't help the situation, because they apply equally well to action on either side of that line.
