Atheism, especially Anti-theism, is simply the result of applied rational thought. Critical thinking is already being taught to students in public schools.
Right now we have two problems, though. First, the teachers and curricula aren't getting through to a lot of kids, which means our teaching strategies aren't working. They probably aren't strict/blunt enough to be effective. I'm not a teacher, nor am I a child psychologist, but the fact that something is wrong is fairly obvious, IMO.
Second, we aren't flunking enough of the kids that just don't get it. I don't care if they get separated from their friends, they'll make new ones. That's what kids do and that's one of the points of public school: to teach social skills. What's more important is a good education. If that means your kid gets held back three times before getting to the 4th grade, so be it. Too many kids are getting a shitty early education and just do not have a firm grasp on any sort of rational thought processes. Take a look at... any fucking internet forum... as proof.
Anyway, Atheism is simply a lack of belief in a deity. It isn't learned because by definition, everyone is born an atheist. Only later are people indoctrinated into a cult. And by that I mean "defenseless children are taken advantage of by their parents and brainwashed." They are quite seriously and literally "mentally raped" and permanent damage is done to their cognitive abilities.