Religious freedom?

"An estimated 350,000 religious congregations operate schools, pregnancy resource centers, soup kitchens, drug addiction programs, homeless shelters, and adoption agencies. These serve 70 million Americans each year and the value of their services are estimated at over $44.3 billion annually." (Interdisciplinary Journal of Research on Religion, Vol. 12, Art. 3 (2016)) This is from a religious freedom brochure. Considering how these "free" organizations are controlled by government regulations and are then manipulated by their grants to continue their work I question how free they are to worship, speak out, to petition the government, or to hold privately beliefs about marriage, education and business.