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Yes. That is the danger as I see it. The ultimate goal is to remove the "dangerous" idea that there is any authority higher than the government.
Newdow has made the statement (paraphrasing here) that not only was he offended by the teacher leading the pledge, but that his daughter has to hear the very word "God" mentioned. Notice also that it's not just enough that the pledge isn't lead by the school, he also wants it changed BY LAW to remove the words so that even students can't mention the foul word as protest:

Newdow said he believes that the Pledge of Allegiance should be completely rewritten so that students and others could not inject "under God" as an act of protest to the court ruling.