According to the website, it's traditional for Notre Dame to invite the sitting President of the United States. Also, it appears that there is a rift between the administrators who did the inviting and those people who are protesting. Those who are making the "uproar" are not the same people who did the inviting.
Why would Notre Dame need "just another ploy to get media attention?" Isn't Notre Dame famous anyway? In fact, negative attention could lose them donations to the college.
Freedom of speech is allowed at Notre Dame. Moral outrage and protest is normal with college students.
It's a Catholic college, so it's not unreasonable to expect them to follow Catholic standards. According to the petition, "'This honor is clearly a direct violation of the U.S. bishops’ 2004 mandate in 'Catholics in Political Life': 'The Catholic community and Catholic institutions should not honor those who act in defiance of our fundamental moral principles. They should not be given awards, honors or platforms which would suggest support for their actions'.”