Nowdays most of us agree discrimination on the basis of race, gender, etc is a bad thing. Some philosophers have put forward the concept of speciesm, ie discrimination the basis of species. So following the example, cant we say that universities discriminate on the basis of talent or knowledge? Or employers discriminate on the same basis when giving a job?
Civil society is founded on two notions of justice: absolute justice and proportional justice, a la Aristotle. Absolute justice applies to all members of society for the reason that they meet certain qualification. For instance, any human objects are guaranteed with basic rights for the reason of being human. Proportional justice is founded on the idea of deservingness: those who work hard or are efficient users of their talents should be rewarded more than talent wasters or unincentivized people.
Historically, people have disagreed on the domains of absolute and proportional justice. The right to vote for representatives, for instance, used to belong to the domain of proportional justice (19th century). Many now think the right to a democratic say (voting right) belongs to the domain of absolute justice. The marriage right of same sex people is only recently viewed as the basic right: previously same sex marriage was viewed as an inefficient use of talents (no offspring).
Naturally, the delineation between basic and non-basic rights is circumstantial, cultural, sociological, political. Now, to answer your question, most present societies view matters relating to knowledge and talent belong to the realm of proportional justice. Thus when universities and businesses treat individuals preferentially based on talent and knowledge, they are not viewed as discriminating people on these bases.
The movement towards the disapproval of discrimination is not equivalent to the elimination of differentiation. The distinction between treating everyone fairly and treating everyone the same is an important one to recognize. The key take away from the change you are describing, is the elimination of bias (or the elimination of devaluing "the other"). Issues of a polemic and orthodox application of egalitarian distribution are apparent in strict institutionalized socialism or Communism. As John Locke and Thomas Hobbs describe, society is formed on the basis of a tacit agreement between individual to create security for the individual and create opportunity through collective efforts and mutual exchange. Oppositely, Marx describes a socialist society, where these roles are reversed - Individuals serve the needs of the community united by a collective struggle.
One of the largest issues with the socialist perspective is that we are not all equivalent, with the same needs, motives, or abilities. It neglects the human intuitions of being individuals first and members of a community second. Historically, the strict application of communism - though rarely expressed in a true adherence to its own values - has resulted in a stifled society. I refer to the collapse of the USSR as a result of rationing and social issues stemming from limitation on individuality. Another example is the collapse of many kibbutzim - the local level socialist communities of Israel. These groups' struggle to maintain a commitment to equality for all, has resulted in greatly diminished participation. Conversely, the competitive nature of the free market and individualism has resulted in higher incentives and greater rewards for both individuals and society.
Intrinsically, scarcity requires differentiation because it cannot provide enough to satisfy everyone. Up until society reaches a point of unlimited abundance - where the maximum of each individual's needs are met by the sheer volume of resources, a healthy understanding of differentiation is important. However, it is equally important to show respect and preserve each individual's dignity by not devaluing them based on differences. Instead, it is important to provide fair opportunity until then.