The programs these churches run are typically filling in gaps in social programs that the government doesn't have the political mandate to enact.
If these churches were taxed you'd see their charities diminished while the funding went to some pork belly spending project, or at the very least not related to what services the church is suddenly not providing.
Not all government spending is a net positive.
... No, it's to grant Biden wider power to retaliate against them for firing at commerical ships in international waters.