If they're taking the reparations from the money they normally distribute to schools, the schools will still feel the pain.According to the article, the NCAA will handle the back payments:
"Separately, the NCAA is responsible for paying about $2.9 billion in back damages over a 10-year period. The funds, some of which could be offset by insurance payments, are expected to come from the NCAA’s annual distribution to schools, mostly from the NCAA men’s basketball tournament (upwards of $700 million annually)."