It is not simply the blatant disregard for the principle of free speech (which is common to all mindsets driven by religious thought -- be it faith-based or secular ideology based, it does not matter). It is that the arguments on which the ban rests, like Professor Khalid points out, are deeply, obscenely DISCRIMINATORY.
It is not just a logical fallacy to assume that one subset of a group represents the whole: it implies the concept best expressed as: "All of them are the same". It imposes on the group a reductive identity determined by the prejudices of the authority that pronounces the statement, whether or not reinforced by vocal advocates of specific interests within the same group.
Racism is the mental attitude that attributes the same character to large groups of people based on vague phenotypes: is racist to assume that all black/coloured/white people (and subcategories thereof) think, feel and behave the same. It is racist whatever the colour of the skin of the speaker.
Religious intolerance is the mental attitude that considers religious beliefs different from one's own evil and to be eliminated, and discriminates people on this basis. Part of the discrimination is the assumption that the very same beliefs are embraced fully by any adherent of said religion.
In the specific case, what Hamline University has done is painting all Muslims with a broad brush, which is shockingly dismissive of Islam while pretending to be respectful. (I am highly critic of Islam -- as well as of Christianity, Judaism, and every other religion Abrahamic or not -- but even when you consider an attitude to be negative, it is a wise course to know and understand it).
Specific interest groups within these wider groups push, loudly, for their own purposes... it is a struggle for of power, and Critical <Name> Theory folks should have read their Foucault better (if even they know where their power rigmaroles come from). Groups are painted with very broad brushes, but who reaps the (temporary) victory are not the broad groups, but individual activists or subgroups that push their own agendas.
The entire Human Rights established regulations are being increasingly hijacked by groups that are bent on silencing dissent using the vague concept of "harm", discrimination and "-phobia".
From many parts they are also deeply conservative and illiberal groups, which happens mostly outside of the West but increasingly here as well, pointedly starting with religion.
Make no mistake. All of these are strategies, conscious or not, that go in the direction of an illiberal society where undesired thought is suppressed. It is not a matter of Left or Right -- this tendency has always existed in both camps. It is a matter of dreaming a society where what is different is NOT allowed to exist. Dreams of this kind are always built on good intentions, a sense of guilt and a sense that what is other than you diminishes what you are.
Let us all look at ourselves and count the number of unwarranted generalisation we make every day, driven by anger. ALL OF THEM, we say. ALL OF THEM. EVIL. WRONG. ENEMY.
And with this attitude, we all go to hell. All together.