I've read through this thread and it seems like most people don't understand that at a religious school, you actively practice the relation on a daily basis and this is why they are open only to children of that religion.
It isn't comparable to a Christian only GP practice 
I went to a Christian school as my family are Christians. We had to pray in the morning, took part in church services, the religious lessons were more catered around bible study, had a Chapel to attend, took communion.
I'm not religious now, but if you're living a very Christian lifestyle, your life can revolve around your faith and that is why my school was like that.
I don't think it would have been suitable for a child of no religion, or a Muslim or Jew to be sat in communion with me.
I don't think it would be enjoyable either!
But for the most part, I don't think the schools aren't letting your children in to be horrible and discriminatory. I think they just want to practice their beliefs without your non religious child taking a place.
I also remember a teacher telling me that Christian parents who had the discipline to attend church every Sunday (we were only allowed to miss 2 Sundays a year to get into my school) were seen as better families to have at the school, because they would push their children harder, be more committed to school events, stuff like that!
I won't be sending my daughter to a religious school, just as a side note. We're not a religious family, I don't want her having to sit through church services if she doesn't want to.