No it isn't. To claim, as many of them do, that religion should be banned from government schools because government should not fund education is a dodge. A typical Libertarian dodge which fits in perfectly with the liberal agenda. One doesn't give up constitutional rights simply because government funds something. Not all Libertarians are this way but many are. You can pin them down by asking about a privately funded Nativity scene on public land. They are against that too. Just my opinion of course but I believe, strongly, that most Libertarians are liberals in disguise.
Should they ever accomplish anything concrete to advance the principles they claim to hold, I will think different. But in 30 years they have done absolutely nothing except talk and pick off an occasional GOP candidate.
I am an atheist, and it is certainly immoral to use money that is forcibly taken from me (i.e., taxes) to promote religion in a public school. Of course, the same injustice applies in your case as well, which is why public schools must be abolished...