I agree, the whole ruse that these 501s meaningfully does charitable work for our communities is laughable and their tax exemption should be revoked, at least with regard to land taxes.
And parking is a productive use - they have services once a week, and parking means people can come to the service. That's the definition of productive use. Something does not need to be used 24/7 to be productive.
Every other contemporary development in my area that faces real economic reality is ground floor retail, commercial/residential on top, and optionally underground parking.
There are certainly productive religious charitable efforts using facilities like this: homeless shelters, community low-cost/free clinics, soup kitchens. I think these uses should be tax subsidized, but other mystical efforts should not be whether they generate a profit or not.
I think a good reform to the 501c3 system would be to make non-profits like these churches and hospitals classify their actual charitable activity and separate it from their other activity, just like individuals with a mix of personal/small business income/expenses are required to do.