You don't have to treat universities and churches the same., the tax code specifically defines which organizations are tax exempt. Churches and universities are

You don't have to treat universities and churches the same., the tax code specifically defines which organizations are tax exempt. Churches and universities are "501(c)(3) organizations", i.e. "Corporations, and any community chest, fund, or foundation, organized and operated exclusively for religious, charitable, scientific, testing for public safety, literary, or educational purposes, or to foster national or international amateur sports competition (but only if no part of its activities involve the provision of athletic facilities or equipment), or for the prevention of cruelty to children or animals, no part of the net earnings of which inures to the benefit of any private shareholder or individual, no substantial part of the activities of which is carrying on propaganda, or otherwise attempting, to influence legislation (except as otherwise provided in subsection (h)), and which does not participate in, or intervene in (including the publishing or distributing of statements), any political campaign on behalf of (or in opposition to) any candidate for public office." You can just amend that law to delete "educational", which would remove the tax exemption for universities, but keep it for churches. It is already the case that there are organizations which don't pay out dividends to owners (so they are "non-profit"), but which are not tax-exempt. One example which has been discussed on Hacker News is foundations set up to accept donations in order to fund development of open-source software.