No doubt; but what individuals do on their own isn't the question here. We're talking about government-imposed religious indoctrination. The real solution is to get government out of the education business, but pending that, government-run institutions shouldn't impose religion on people.
If you believe that speaking the pledge in the presence of one atheist second-grader is imposing religion on that child then by preventing the pledge to be spoken the Judiciary is imposing atheism on the Jews, Muslims and Christians in the same classroom.