2. If you're going to tax non-profits, then why have non-profits?
3. Do we really want to penalize fiscally responsible organizations when even governments are going bankrupt? What values are we trying to support here?
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.
Right. There are some very wealthy churches. In the United States alone, the Catholic Church has an operating budget of $170 billion. That's bigger than Apple.
I think it's worth noting that over $147 billion of that number is spent by Catholic hospitals ($98.6 billion) and universities ($48.8 billion). The number more representative of what most people mean when they refer to "churches" would be Parish disbursements ($11 billion). $11 billion is nothing to sneeze at, but when you consider that there are about 17.5k parishes in the US (many of which have schools) it's a less impressive number.