ZD,
Making money does not it make a commercial enterprise.
There is a distinction between a commercial enterprise and a non profit even though a non profit still has to make money.
Further, the real estate tax exemption extends to when the non profits uses the property for its exempt purpose. So renting out student and faculty housing is not a commercial enterprise that would be taxed, it is part of the exempt function.
If they rented out to stores or regular commercial office space, that would subject the property, or the allocable portion of the property to tax.
In downtown Manhattan, Trinity Church is one of, if not the biggest commercial real estate owners. The properties are not exempted just because they are owned by an exempt entity.
What is clear from your comment is that you really don’t know the nuances related to not for profits if you would not know the difference between commercial enterprise and program related revenues.