Paying one's respects can and should be voluntary. I have nothing against that.
Of course there's more to totalitarianism than just coerced loyatly oaths. Totalitiarian states disrespect the rights of their inhabitiants in a number of ways. However, coerced (the part you conveniently forgot to address) loyalty oaths are a defining characteristic of every oppressive state I can think of.
I agree that children should be able to opt out for any reason if they so desire. But I see nothing wrong with the continuation of the tradition of requiring children to stand respectfully before the flag and say the Pledge. It reinforces discipline and order in the classroom and reminds children from whence comes their educational benefits and other benefits of a cooperative society.
There was an opt out clause. You people get upset about the silliest things.