I'm sorry - you mean to tell me that the inclusion of two words - "under God" - means that schools are endoctrinating religion!? Would you kindly tell me what religion that they are promoting? I would insist that most (if not all) religions have a single God (or god, if you insist) at the head of whatever pantheon that is central to their belief structure. The pledge acknowleges that fact, by not singling out the Christian nor Jewish nor Islamic nor any other perception of God.
I would say that this father is wrong to impose his beliefs on the masses.
In the Florida case (which the father lost by the way), the school offered the opportunity for his child to step out of the room or otherwise be excused from saying the pledge. The father insisted that this was not good enough, because his child should not have to listen to others recite the pledge in school. Hence his decision to move across the country and to bring his suit in a different court.