Of course it's an honor, a coup even, to get the President to speak at commencement. However, sometimes it's just not appropriate.
For Catholics, no issue plays bigger in the media than abortion (that doesn't explain why Catholics vote in large part for Democrats, but that's not the subject of this post). So to have the President give the commencement address at a Catholic university seems odd to me. It's not hypocritical, as some suggest, but one wonders why Notre Dame would choose a graduation speaker that stands in stark contrast to one of their most cherished values.
Yes, it's an honor to have the President speak at your school, but in a case like this, it also grants a certainly legitimacy to the President. I completely understand why some, like the ones in this video, would think this is a bad idea.
Some students may boycott their own graduation over this. That strikes me as silly and overreacting. A tasteful show of disapproval would be warranted, perhaps wearing black armbands or something. Not clapping when the President speaks would also be appropriate. Booing, standing up and turning their backs as the President speaks, disrupting the speech--in other words, actions we've learned from lefties--would be highly inappropriate. The selfish, immature, "look at me" nature of such acts precludes their use in polite company, and a university graduation certainly qualifies as "polite company".
I hope everyone involved acts accordingly. The head of Notre Dame has already screwed up his end of the bargain by inviting the President to speak; the students don't have to screw up their end.