In the case of religious organizations a lot of their assets weren’t purchased primarily as investments. Most religious organizations largest assets are in real estate sitting under their churches. The real estate may have appreciated over 100 years but taxing a church on “gains” when the building needs to be moved to make way for an office building isn’t generally what people think of as investment gains.

The same can be said for most charitable organizations. The community food pantry being taxed if it moves across town or simply trying to keep the rainy day fund even with inflation.

If a person is of the view that all good things come from the government then taxing charities makes a lot of sense. If, on the other hand a person believes that all good things originate from the people and that the government is just one of those good things it makes sense to allow room for other things that serve the people’s interests but don’t directly serve the governments interests.

I am certainly not saying that bad things don’t come from religious organizations, charities or the government. I am saying there is a belief in the US that power ultimately resides with the people. Actually with the people, not the government or through the government as representatives of the people.