There is no science behind this decision. There has not been any evidence to suggest that a newborn will contract a virus that the mother is carrying upon intake.
In fact, if you think about it, by the time mother shows symptoms, the antibodies are rampant in her system...and thus in baby's system. Therefore, its highly unlikely that baby will contract anything the mother already had prior to the birth, especially if she breastfeeds.
Also, don't you think that its more likely the baby will get it if father gets it from mother, the virus mutates slightly, and then HE gives it to the baby while feeding?
Plus, I know health practitioners that just wear masks and use hand sanitizer when they have any kind of influenza (which is proven worse, overall, than H1N1) rather than not go to work. Why can't parents just do the same?
I think the concern is more legal than health safety, here. If a child gets sick (no matter how) and dies, the parents will sue. The hospital has the obligation to prove that they did everythign necessary in the event a child contracts an illness like this in their care. Since there is no science to suggest really how things work one way or another, they have to err on the side of caution...caution for their own financial backsides.