The problem was not that the five churches rented out worship space at public schools -- that's perfectly legal -- but that there was evidence that the churches had not paid fair rental price for about six years, thereby shortchanging those schools up to $5,600,000. (One of the schools that was owed more than $3,000,000 could've used that money after it had a roof collapse.)
MORE: http://www.patheos.com/blogs/friendlyatheist/2014/02/15/atheists-lawsuit-against-churches-that-deprived-public-schools-of-5600000-finally-results-in-partial-recovery/