My uncle is Newdow (the guy who sued)'s lawyer Bummer that they lost though...
apparently 3 of the justices made a concurring opinion and said that even if they had ruled on the case based on its merits (the father's standing aside), their decision would not have changed.
To take a case to court - you have to have the legal standing. You can't take your neighbor to court because he hit someone else. You can only take your neighbor to court if he hit you. When it involves a child, the parent that has the legal responsibilities for the child (in this case the mother) is the only one that can bring lawsuits on the child's behalf. Now, if the father gets joint custody, I bet they can retry the case...