It almost certainly was intentional that they showed CM as the narrator says "...and those whose opinion we reject." Interpreting it charitably, it's great that they open the ad with a quote from Aquinas. If the goal is to tell people, "You'll read a broad range of things at ND, but analyzed through a Catholic lens and only after receiving a solid foundation in Catholic thought," then I'm all for it.
The problem isn't that message, but that we don't actually do that anymore. In 7 straight years at ND, I was never assigned Aristotle, Augustine or Aquinas; Dante, Chesterton, Waugh, O'Connor, or Tolkein; never asked to read an encyclical or the decrees of an ecumenical council. The Church's perspective on various issues was rarely brought up, and if it was, it was simply presented as one opinion among many. The hiring of faculty is handled almost entirely at the department level, and whether or not a professor is a practicing Catholic means very little compared to things like academic prestige, # of citations in peer reviewed publications, etc. The First Year of Studies program, the "core" curriculum that every ND student ought to receive before graduation, is a pale shadow of what it once was, and is still under constant attack.
There are more Catholics in America than any other single religious denomination, and ND is unarguably the flagship Catholic university in this country. But once you take away that religious character, we're just another small liberal arts school in a cold demographically-declining part of the US scampering for scraps from the Ivy League table. Yet our leadership has been actively undermining that most important part of our identity for decades.
I'd happily cheer for an ad as described in my first paragraph above. Unfortunately, I think the intent was more along the lines of: "Notre Dame, where you'll read the same shit everyone else does."