The issue with religion (i.e. creationism) in schools is that they're not too even handed with it. It's pretty much creation theory from the christian standpoint and that's it--maybe if you're lucky and live in New York or LA they put a jewish slant on it.
To me the biggest problem is that Americans don't want their kids to be critical thinkers (as a general rule). Everyone wants their kids to be smart, but with intelligence (book, street, or other), also comes questioning of "why". More often than not that "why" happens before parents or other authority figures think they are ready (news flash: they are ready when they start asking about and questioning it). Instead of being good, little obediant children who honor, obey, and respect their mother, father, and teachers; they start to think for themselves and draw their own conclusions which are ocassional completely different from, and opposite to what the authority figures think they should be--and the authority figures can't handle it--either the lack of homogeny scares them or the realization that the kids are smarter than them and can articulate their stance better scares them.
IMHO it's bullshit.