However, if the government is going to run public schools, then those schools must serve the whole public, not just a part of it. It's not acceptable for the government to tax 100% of the population and use the money to run schools that serve only 80% of the population. The compromises that the school system makes to do that are, for the most part, reasonable.
Yes, it's too bad that the small minority does lose out in some way, but that's price that's paid for a government-run school system. So unless courts are prepared to declare government-run schools unconstitutional on the grounds that they necessarily interfere with somebody's religious liberty, then they have no business favoring one group's sensibilities over another's.
The courts aren't going to do that though. Why would they tear down the entire edifice of the public school system when they can simply throw out the part that's biased towards Christianity?
As I said, bias is inevitable. Either you're inconveniencing the theists, or you're inconveniencing the atheists. The courts have taken sides, and that's unfortunate.