Church-run charter schools are foolish and dangerous
With government money comes government strings, and those strings are a danger to religious liberty.
Vox is worried that a Supreme Court case could erase the "wall of separation" between church and state: Will a Roman Catholic charter school be approved? The Supreme Court has ruled that government may not discriminate against religious organizations applying for money that is publicly available, but having a public charter school operated by a church (whether Roman Catholic, or any Protestant denomination) is a significant further entanglement of church and state.
I have been warning about vouchers for decades. When private schools take money from government, there is always a risk that the government will use that money as leverage to get the schools to do what they want. Either the schools will be forced to hire teachers and staff who are openly engaged in sinful lifestyles contrary to church doctrine, or they will be forced to hire people who openly reject Christianity, or the government will attempt to force the school to change curriculum and doctrinal stances. This is also why I opposed President Bush's plan to give money to faith-based charities in 2001.
The danger of that is heightened when a Christian school is made into a charter school. While charters do have more freedom to operate than traditional public schools, they are under state oversight that is (currently) more strict than schools that take private school vouchers. Do we really want to risk government having direct control over the curriculum and doctrine of a Christian school? We are increasingly living in a post-Christian culture, and we have many people in our government who are openly hostile to Christian doctrine. Even the "Republican" superintendent of public instruction in Indiana (elected statewide in 2016) called for more strings on private schools that take vouchers, and both the incentive to do that and the legal justification to do it will be much more intense at a tuition-free public charter school approved by state government.
This, of course, will not just be applied to hiring faculty and staff. Can a student who is openly hostile to Christian doctrine or openly living a sinful lifestyle be excluded from a Christian charter school? Private schools have significant leeway in removing disruptive students, but the hurdle is higher for public schools due to every child and teen having a right to a public education. Charter schools - at least in Indiana - are not permitted to discriminate based on belief, but having a student (especially in high school) openly hostile to Christian doctrine could be a disruption and a spiritual danger to other students.
Charter schools are good, and an important aspect of public education. They fill the needs of many students in ways that traditional public schools cannot. Explicitly Christian schools are taking a significant risk when operating charter schools, though. Christians should not risk our religious liberty and doctrinal commitments in order to get a few dollars from the government.