The way I look at it, schools have a duty to teach facts as facts, and opinions and opinions to be critiqued.
Fundamentalist Christians demand that evolution not be taught in schools. Shockingly, in the USA this is actually listened to in some place, thankfully not here. So evolution is taught as fact given that all credible scientists are certain that all the evidence backs it up. Creationist theories are taught as just that, a theory. This religion believes in Adam and Eve etc. This is not backed up by any evidence, so science ignores it.
RE children should learn about all the major religions, what they believe and why they believe it. It helps understanding and tolerance.
Similarly, social issues should be taught as, well: certain people are attracted to people of the same sex. They can live together and be married. In the UK we now believe that this is valid and ok. They are born with this preference and they deserve our respect. Some religions teach that it is not ok. Gay people have been treated badly because of these teachings. In a civilised country like the UK, you can disagree with their choices, but you should respect them and treat them equally. This is actually the law.
If you are muslim, for example. I don't think you can possibly ask that children learn about your religion so that they develop a knowledge and erespect of your religion, then in the same breath exclude their own children from learning the same tolerance for other peoples life choices.
Just to add my opinion in here some more. Homosexuality is something you are born with. Its not really a choice. Religion is a belief system. Like following a football team that that is just a bit more historical. As a society i don't know why we give so much credence to ancient texts and the beliefs of their followers, but i suppose we have to for the sake of peace.