Why are atheists allowed at a Catholic university?
For the same reason that many Muslims attend Catholic universities and high schools — education.
The tuition check clears the bank just as quickly as any written by a believer.
That, and the Church is naive about the threat this poses to the academic freedom and spiritual milieu of the university.
I think many people think of atheists as skeptical, but nevertheless civilized and non-violent. That’s less frequently the case these days.