I'm all for peoples individual rights to teach their children whatever they want so long as the schools are privately funded. Schools receiving public funding should not be allowed to operate with such discriminatory regulations.
In my opinion, there are some good arguments against private schools. First is the indoctrination of children being homeschooled by fundamentalists, especially with regards to evolution and science (as we saw in Jesus Camp... I wonder if private religious schools in Canada have any of the same issues). Also, there is an argument to be made against elitism with regards to certain children gaining benefits such as scholarships and a better chance of getting into prestigious universities by going to prestigious schools.