As long as there are public schools, there will be public school rules. Children who go to public schools must follow public school rules. If you don't like the public schools, there are private schools. There is homeschooling in most states.
A lawsuit by a Pennsylvania atheist parent and the American Atheists group demands that an atheist child get a religious exemption from a school-uniforms policy. The lawsuit claims that the uniforms "hinder her children's creativity... and freedom of expression" and are militaristic, too, which the mother opposes.
As a public school teacher, I "hinder my students' creativity" every flipping day when I stop them from drawing Japanese-style fighting cartoons when they should be reading. I also hinder their "freedom of expression" by telling them when they may and may not speak and what they may and may not talk about. Schools have to be able to set rules and enforce them to function.
If there is a rule that anyone can opt out of for any reason they choose, then it isn't a rule. The Constitution protects the free exercise of religion--access to a public facility such as a school cannot be denied or limited as a result of someone's religion or the demands of that religion. That means that if someone's religion says that they wear all black without buttons, or a skullcap, or a turban, or a feathered headdress, then public facilities must admit those costumes and headgear. Atheists' personal views, however, are not religions, they are personal views. Personal views, if they are not religiously based, are not the free exercise of religion and they do not have to be accommodated in the public schools. A child who is a Jehovah's Witness does not have to stand for the Pledge of Allegiance. A child who simply hates America does. This is why we require the signature of a minister, to have a standard for denying frivolous exemptions.
The suit raises an equal protection claim, that anything religious folks get, atheists should get. Religious exemptions are exceptions to rules based essentially on the fact that a religion claims that to follow the rule would cause God to be angered and smite them. The religious exemption protects the believer from the smiting. Only incidentally does it exempt them from the rule. Whereas if God is going to smite an atheist, it's probably not because I didn't wear the proper hat. Reason does not enjoy the constitutional protection that religion does. Fortunately, we don't need it.