This sums it up fairly well–

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If you want to find (for example) anti-Shiite prejudice, you look at Sunni institutions (and vice versa).  In the same way, prejudice against one specific expression of Christianity is almost invariably going to come from other branches of Christianity, and usually the more reactionary and exclusionary ones. 

Frankly, reading over the stuff about Bob Jones just reminded me how much they truly do not want to know who Jesus really was, and what he really taught.  And this is not me saying that Catholicism has that 100% right, but the Bob Jones’s of the world have it almost 100% wrong.  There’s really no keeping up with them.  😉

A lot of people in secular academia are Catholics.  And lots of people with no connection to academia may have issues with the Catholic Church and/or certain ethnic groupings that are identified as Catholic.  I really am not sure what you’re asking here.  But I would say that it would be most odd for a secularist to be prejudiced against Catholicism only.  I can’t say offhand I’ve ever encountered that.  And if it’s a prejudice against religion in general, then how would it be anti-Catholic in particular?

I’ve given you a clear example of an institute of higher learning (or so it claims) that is out and proud in its contempt for Catholicism.  You don’t seem interested.  Because you were fishing for something to use against secular academia?  Sorry to disappoint you. 

If there’s one thing Catholics should be proud of, it’s the incalculable contribution of their Church to higher education and the furthering of human knowledge over the past millennia and change (in spite of the occasional misstep, pace Galileo).  So why treat higher education as the enemy, when it has been the means whereby immigrants of Catholic faith have raised themselves up in the world?  Knowledge may be a religious fundamentalist’s enemy in some cases–Catholics are not fundamentalists, and most real anti-Catholic prejudice stems from fundamentalism. 

So a sectarian war against ‘academia’ is okay?  Nobody asked you to start anything at all, you know.

I went to CUNY Graduate Center for several years.  I never caught even the slightest whiff of anti-Catholic prejudice there.  And one of my courses was on the Reformation. 

When you talk about ‘secular’ academia, do you actually mean Jewish?