Parents have a right to freely choose their own educational options for their children, whether the parents are muslim or Christian or anything else.
In the United States we usually have the homeschool parents meeting basic curricular guidelines so there are some standards which allow home-schooled children to successfully meet standardized achievement tests and college entrance requirements.
Speaking as a former public school teacher who also worked with home-schooled children, the home-schooled children I know are, without exception, more articulate, polite, intelligent, and self-assured than their public school counterparts.
They would certainly keep their children form a publicaly and open disputed and discussed form of education.
Why would indoctrination be any easier in a public ond open form of school then in the cellars of some private entities ?