Here's an article about "an increasingly popular tax credit program that transforms state money into private school scholarships, some of them used at religious-based schools that prohibit gay, lesbian or bisexual students from attending" in Georgia. A report says that "public money is being spent by private educational institutions that “p'unish, denounce and even demonize students in the name of religion solely because they are gay, state that they are homosexual, happen to have same-sex parents or guardians, or express support or tolerance for gay students at school, away from school or at home.'"
There are similar tax credit programs in eleven states, and the program "is intended to avoid conflicts between church and state because the money is collected and distributed by nonprofit organizations." But there is little state oversight, and the money is clearly going to schools which practice blatant discrimination, at least in Georgia. What's more, a state representative in Georgia intends to push for the state funding for the scholarships to rise to $100 million this year.
A Democrat state representative puts the problem succinctly: "“We are circumventing our own public policy with public money."