Marcuse worries that by being tolerant of things that are clearly oppressive and unjust we misuse the idea and produce the opposite effect that we intend. I have seen many variations on this idea expressed here but it is always good to look back to a scholar who really worked at understanding it. He begins:

THIS essay examines the idea of tolerance in our advanced industrial society. The conclusion reached is that the realization of the objective of tolerance would call for intolerance toward prevailing policies, attitudes, opinions, and the extension of tolerance to policies, attitudes, and opinions which are outlawed or suppressed. In other words, today tolerance appears again as what it was in its origins, at the beginning of the modern period--a partisan goal, a subversive liberating notion and practice. Conversely, what is proclaimed and practiced as tolerance today, is in many of its most effective manifestations serving the cause of oppression. The author is fully aware that, at present, no power, no authority, no government exists which would translate liberating tolerance into practice, but he believes that it is the task and duty of the intellectual to recall and preserve historical possibilities which seem to have become utopian possibilities--that it is his task to break the concreteness of oppression in order to open the mental space in which this society can be recognized as what it is and does.

Tolerance is an end in itself. The elimination of violence, and the reduction of suppression to the extent required for protecting man and animals from cruelty and aggression are preconditions for the creation of a humane society. Such a society does not yet exist; progress toward it is perhaps more than before arrested by violence and suppression on a global scale. As deterrents against nuclear war, as police action against subversion, as technical aid in the fight against imperialism and communism, as methods of pacification in neo-colonial massacres, violence and suppression are promulgated, practiced, and defended by democratic and authoritarian governments alike, and the people subjected to these governments are educated to sustain such practices as necessary for the preservation of the status quo. Tolerance is extended to policies, conditions, and modes of behavior which should not be tolerated because they are impeding, if not destroying, the chances of creating an existence without fear and misery. This sort of tolerance strengthens the tyranny of the majority against which authentic liberals protested. The political locus of tolerance has changed: while it is more or less quietly and constitutionally withdrawn from the opposition, it is made compulsory behavior with respect to established policies. Tolerance is turned from an active into a passive state, from practice to non-practice: laissez-faire the constituted authorities. It is the people who tolerate the government, which in turn tolerates opposition within the framework determined by the constituted authorities. Tolerance toward that which is radically evil now appears as good because it serves the cohesion of the whole on the road to affluence or more affluence. The toleration of the systematic moronization of children and adults alike by publicity and propaganda, the release of destructiveness in aggressive driving, the recruitment for and training of special forces, the impotent and benevolent tolerance toward outright deception in merchandizing, waste, and planned obsolescence are not distortions and aberrations, they are the essence of a system which fosters tolerance as a means for perpetuating the struggle for existence and suppressing the alternatives. The authorities in education, morals, and psychology are vociferous against the increase in juvenile delinquency; they are less vociferous against the proud presentation, in word and deed and pictures, of ever more powerful missiles, rockets, bombs--the mature delinquency of a whole civilization.

In any case, John Stuart Mill, not exactly an enemy of liberal and representative government, was not so allergic to the political leadership of the intelligentsia as the contemporary guardians of semi-democracy are. Mill believed that 'individual mental superiority' justifies 'reckoning one person's opinion as equivalent to more than one': Until there shall have been devised, and until opinion is willing to accept, some mode of plural voting which may assign to education as such the degree of superior influence due to it, and sufficient as a counterpoise to the numerical weight of the least educated class, for so long the benefits of completely universal suffrage cannot be obtained without bringing with them, as it appears to me, more than equivalent evils.[5] 'Distinction in favor of education, right in itself', was also supposed to preserve 'the educated from the class legislation of the uneducated', without enabling the former to practice a class legislation of their own.[6] Today, these words have understandably an anti-democratic, 'elitist' sound--understandably because of their dangerously radical implications. For if 'education' is more and other than training, learning, preparing for the existing society, it means not only enabling man to know and understand the facts which make up reality but also to know and understand the factors that establish the facts so that he can change their inhuman reality. And such humanistic education would involve the 'hard' sciences ('hard' as in the 'hardware' bought by the Pentagon?), would free them from their destructive direction. In other words, such education would indeed badly serve the Establishment, and to give political prerogatives to the men and women thus educated would indeed be anti-democratic in the terms of the Establishment. But these are not the only terms. However, the alternative to the established semi-democratic process is not a dictatorship or elite, no matter how intellectual and intelligent, but the struggle for a real democracy. Part of this struggle is the fight against an ideology of tolerance which, in reality, favors and fortifies the conservation of the status quo of inequality and discrimination. For this struggle, I proposed the practice of discriminating tolerance. To be sure, this practice already presupposes the radical goal which it seeks to achieve. I committed this petitio principii in order to combat the pernicious ideology that tolerance is already institutionalized in this society. The tolerance which is the life element, the token of a free society, will never be the gift of the powers that be; it can, under the prevailing conditions of tyranny by the majority, only be won in the sustained effort of radical minorities, willing to break this tyranny and to work for the emergence of a free and sovereign majority - minorities intolerant, militantly intolerant and disobedient to the rules of behavior which tolerate destruction and suppression.

In other words we are are being had with the modern notion of tolerance. Given that we are making headway as we fight for civil rights, etc., we are doing so with a handicap. The very value we wish to achieve has been so badly distorted that it often works against us. Do you have examples in mind? How about "religious freedom", "2nd amendment rights", "the freedom to exclude people who are different", "the rights of a fetus", etc. Why are we progressives so intolerant? Marcuse goes on to sayIt is interesting to ask as you read his words: "How much has changed since then?" The answer kind of makes his point. Read the whole essay. Here's how he ends:I maybe intolerant in other's eyes but there is some stuff I will not eat!