First, congratulations on finding another topic to post on.
I'm not familiar with the National Day of Prayer or what the school was doing. Part of the problem with public schooling is that it's government sanctioned and thus you get this whole church/state conundrum. If people were reasonable and level-headed, those who didn't believe in prayer could just be silent. But there is always (a) a jackass parent who complains that their child is being forced to pray, or (b) a jackass teacher who forces a kid to pray or ostracizes a kid who doesn't.
Sadly, the peripheral d-bags force the issue and courts have to get involved to remove a relatively harmless "day" from the schools.
If you choose public schools for your kid, this is the BS you buy into.