No obviously where a child is abused sexually, physically -- the state has an obligation to seperate the child from his/her parents. Otherwise yes, parents have ultimate autority over children regardless of how they use that authority.
There is no way to argue that the state has the right to seperate a child from his parents where there is no physical or sexual abuse. And especially not over anything as trivial as politics.
As a point of fact, every followup story on Elian I've seen or read has indicated that he's grown up pretty happy and healthy, maybe for no other reason than for propaganda purposes but there's also no way to argue that sending Elian back constituted abuse.