ACLU attorneys risk not being paid only in cases they lose. In cases where a citizen establishes that government action infringed upon a protected right, his attorney fees and court costs are assessed against the losing government unit.
I'm not mistaken.
The original question was why did the ACLU charge the parents to take the case. The ACLU did not charge the parents to take the case. They did it pro bono. Now if they can get paid by the losers after the case that's their business. But the the ACLU lawyers worked pro bono in the first place.