It's because it does matter to the outcome, if you consider the outcome to be more than just GPA. GPA is not the best indicator of whether it's a worthwhile investment. The selection of a private school takes in to account additional factors like the environment you learn in, the connections you make, the college prospects you get and also the mere existence of religion.
Private schools are often affiliated with religious groups (Catholic, Jewish, etc.) For many people who choose private education, the existence of religion classes in school is a large factor.