The First Amendment prevents government from discriminating against religion.

The New York Times, 

Church-State Law, and Equality

by Andrew Lewis

Prohibiting religious schools from using public facilities would not protect religious freedom; it would encourage further discrimination against religion and religious people.

Every week, hundreds of religious bodies use space in public school facilities for their worship services. Indeed, approximately two percent of all religious congregations, according to the National Congregations Study, do this.
Churches using school buildings seem to be a recent phenomenon, potentially due to the fracturing of American denominations, the growing preference for casual, low-church facilities, and the desire to reduce operating costs and allocate more resources to ministry. In some locales, churches may be renting school space because zoning laws prohibit tax-exempt churches from buying and using land that would otherwise yield tax revenue.
No matter the reason, this generally happy accommodation between religious organizations and public schools is controversial, and even heretical, to some who seek to sanitize public life in general--and public schools in particular--from religion.
The New York Times and the ACLU Don't Understand the First Amendment
An outcry against religious groups using public schools has resurfaced in the pages of the New York Times. On May 24, the Times editorial board declared: "Get Churches Out of Public Schools." They argued that allowing churches to use public school facilities when school is not in session "could turn public school facilities into houses of worship, essentially funded by the government." Citing the New York Civil Liberties Union, the New York affiliate of the American Civil Liberties Union, the Times asserted that prohibiting religious organizations from using public schools would protect religious freedom.
But this line of reasoning gets the First Amendment's protections for religion backward. It restricts individuals and groups, not governments. It seeks to privatize religion and protect society from religion, not promote religious exercise and leave room for it to compete in public life. An application of this principle would damage religious life, especially smaller religious organizations.

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