My grandpa can't help how the pledge of allegiance was when he was in school.
My point being that for the longest time, God wasn't mentioned in the pledge. It didn't make Americans less American or less religious. Honestly, I don't care if it's in there or not, but I've got no problem with people who don't believe in God, but love America to leave that part out of the pledge. And for people who have something against America or pledges in general to stand silently. (though I do have issues with people that make a big deal out of NOT saying the pledge during the pledge)
Parents are no more likely to "know best" than bureaucrats. Get rid of sh**tty bureaucrats, sure, but putting parents in charge of school decisions isn't going to end well in a lot of places.
While I agree with you here, I don't think these things happen all that often (if ever). If you think they do, you'll need to give me a cite.
How could it be taken away? Prayer doesn't have to be a show, it can be a silent conversation between you and your god. Kind of hard, nay, kind of impossible to take that away.