I don't understand why they are necessary. If you want to be religious you can go to church. Schools should be a secular environment for learning.
If someone is teaching you from a religious point of view, then what they teach you will be biased, whether implicity or explicitly. I know most teachers in religious schools are careful not to be biased, but there are still classes like Religious education which do this. Children should be able to learn in an environment where they can form their own opinions, uninfluenced by religious doctrines and unrestricted by religious taboos. If religious biases exist in schools, it is more likely that children will grow up to believe that since schools are places of authority, those particular religious biases must be the truth.
In addition, schools based on religion (or for that matter, race) only encourage segregation, at a time when it is especially important for kids to recognise the values of egalitarianism - but in reality this is only a very slight issue.
The main point here is that school and church should be separate.