Nobody believes in tolerance as a virtue
Nobody on the face of the planet believes that tolerance is in and of itself a virtue, and nobody has ever believed that. Not one single person in human history has ever been perfectly tolerant, and nobody should be perfectly tolerant. We need to reject the meme that tolerance is always good, breaking free of this sophistry to instead think like men and women, not little children.
Instead of extolling the virtues of tolerance itself, we should think about what should be tolerated, and what should not be tolerated. Obviously, things like murder, rape, stealing and terrorism should not be tolerated and even those who advocate for "tolerance" most loudly will agree with that. Christians are expected to not tolerate sin, either in our own lives or in the world around us. So the first distinction we need to make is the difference between a sin and a crime. (For the purpose of this discussion, crimes are the most serious sins. Not all crime is sin, and that is a separate issue to be discussed at a later time.)
A crime harms someone else and must be punished by the civil magistrate. Sin primarily harms the sinner, though it may cause harm to someone else that does not rise to the level the civil magistrate needs to use the sword. Because we are called to love God and His Law, Christians should not "tolerate" things like greed, anger, pride, bitterness or lust. We should rebuke sins, with the hope that either the sinner will come to repentance and faith or that we will have victory over it. But it is not a crime to be greedy, angry, arrogant or lecherous unless the idolatry in a man's heart leads him to commit actual physical crimes.
In fact, sometimes tolerance is objectively evil. When people in positions of authority know terrible crimes are being committed and innocent people are being subjected to horrific acts and then do absolutely nothing to stop it, those in authority are every bit as guilty as the criminal himself. In fact, it could be argued they are actually worse because they refuse to use the authority given to them by Almighty God to protect the widow and the orphan. Tolerance is never admirable when we tolerate helpless innocents being victimized.
We live in a nation that, as a matter of law, tolerates all manner of religions and political ideologies. We live under a constitutional system that does not jail or execute people for their religion or ideology, and that is a good level of tolerance. Christians should then emulate the tolerance in our legal system for those holding heretical or idolatrous religious views, and also tolerate ideologies might find abhorrent. This means we may not harm or persecute people for these reasons. That is why we may not, as the meme goes, "punch a Nazi."
But we are well within our rights to speak against them and try to persuade people to turn away from heresy and idolatry. We are to be intolerant of something that dishonors God, but also being tolerant at the same time within our legal framework. There is not a thick black line where tolerance is universally good or bad.
Obviously, it is impossible to explore every single permutation of when tolerance is good or bad in a blog post. I could write several books on the subject and barely scratch the surface of every possible permutation of this principle. My point is we need to have a broader view and understanding of tolerance and when it is necessary, when it is good and when it is evil. I admit that I am still figuring this out in my own mind. We all are.