It was a private school run by the Church, but Muslim students received Islamic religious instruction.
Obama/Soetero was pulled out of this school and placed in a “public” school later when his step-father deemed that he wasn't receiving enough instruction in Islam. He even took Koranic studies in Arabic, something very few Indonesian Muslim students do.
Every Moslem student on Earth who has a father who attends a mosque is given lessons in Classical Arabic so that he can understand the standard prayers, understand the call to worship, and read the Koran (to a certain extent).
So why would Indonesian Moslem kids be exempt?