I’ve seen this belief stated a dozen times here that churches do all sorts of great charitable work in their communities. Actually they spend less than 6% of revenue on programs that benefit others. The vast majority of church budgets go to salaries and facilities (overhead) and the vast majority of the benefits are enjoyed by the members. Churches have a business model that looks more like a country club than, say, the Red Cross or Rotary Club. There are college fraternities that apply more of their revenue to social service, and corporations that rival churches in their charitable giving.
https://holysoup.com/the-shocking-truth-of-church-budgets/
In my town we have several thousand churches and maybe a half dozen of the much-celebrated “soup kitchens”. Some of these kitchens require religious participation as a condition of receiving food. The number of congregations paying for billboards and TV broadcasts is greater.
So yes, churches are a different type of thing than a nonprofit altogether. Unless you consider religious activity to be a charitable good in itself, they aren’t charities.
The tax code made them this way.
This is not a crazy point, however, you're missing a lot of the nuance. I skimmed the article that you copied, but I'm wondering if you read the comment section, because it provides a great counterpoint to the overall concept that I'll copy here:
"While I agree that congregations need to better spend their money, your comparisons are way off. How can you compare charities that have millions in donations with a congregation that takes in only 40, 000 to 60, 000 in donations. Of courses their percentages are lower."
Percentages can be skewed with larger donations (shouldn't be a foreign concept, it's the whole MMM mindset of don't brag on yourself for saving X percentage, talk about how much you actually spend because if you're saving 25% on $500k salary...not that impressive), and yes, the fact that a huge majority of churches are trying to maintain existence means that the percentages of money that goes beyond subsistence is going to be affected.
I'll give you another example, as well. A church I was involved in performed a children's clothing giveaway. The church had an attendance of around 15-20 and donations of around 40k. It was operating at subsistence levels. The money spent on the children's clothing ministry was still a small percentage of that budget, but that was not indicative of the help provided. First, it was subsidized by many, many volunteer hours to go to thrift stores, sort through clothing in bulk to get the right kinds, and buy the clothing by the pound, purchased very cheaply because of this aspect. Secondly, for a church of 15-20 people - really around 10-12 adults, literally dozens, probably 100+ of families were helped a year with free children's clothing. Churches, especially small ones, are very thrifty and can get a whole lot more bang for their buck on helping out people because of thrift and willingness to volunteer beyond the money by people that can't support as much financially. Again, things like that are the nuances that are left out of the above perspective.