Atheists, it is said, don't want to indoctrinate their children into atheism. Like all blanket generalizations, this likely isn't true. Just as there are parents pounding the fear of god into their kids, there are likely many parents giving the opposite message: you'd better not start believing in god(s) or else....!
The goal isn't to make kids atheists, or a-conservatives or a-liberals or a-discoists. No parent should be teaching kids what not to believe! Instead, a rational goal will be to teach kids how to believe. In other words, arm them with tools that help them to determine what is worthwhile believing in and what is not.
Kids need to learn skepticism. They need to learn to question what they are being told. To be highly suspicious if someone tells you to believe something "because I say so!" To distinguish between theory and idea, fact and speculation, truth and a lie.
Skepticism, though, is very difficult. We need to understand truths about reality to interact with it. If I go near the edge will I really fall off? Is there a lion behind that bush? Always assuming the worst (I will fall off; there is a lion) leads to mental paralysis and paranoia. We have to build some trust that we have some answers.
Religions, I believe, evolved partly from this. Through experimentation (scientific!) people began to learn about the hazards of a cliff (edges can crumble; it's windy up there) and decisions are made that cliff edges are, indeed, dangerous. Instead of constantly testing the cliff (ok Bob, it's your turn to stand on the edge) those in charge declare it dangerous and tell children not to question the wisdom passed down from our ancestors lest they be killed. We are commanded to respect what the authorities say.
Side note: It's easy to see how heroes can be created by challenging rules. Only the bravest, strongest members can take on the lion and survive leading to heroic tales of how Bob killed the lion (Paul, John, Xavier, Mordecai, Wilma and Betty didn't, so are forgotten by history).
Today's society is challenging the authorities themselves. However, the pendulum is swinging too far to the left. Challenging authority seems to mean 'disregard authority'. Examples of this are running rampant in public schools. Children seem to have little sense of authority and openly defy their parents and teachers, "You're not the boss of me!"
We need to teach children that authorities are required. Someone has to be in charge, someone has to create rules and someone must enforce them. Civilization is defined by rules that allow large groups of people to interact peacefully. We must stop on red. However, the true goal of our enlightenment is to discover that the chickens, not the farmer, rule the henhouse*. God doesn't make the rules, we do. Most importantly, we can question the rules and we can change them.
Science is the greatest tool we have for discovering truths. And from this discovery we can establish better rules. Law allows us a method for creating, enforcing and changing them. A free and just society is one that has this ability.
So, teach your children to ask questions about the rules but please teach them to abide by them. Show them that there is a proper way to challenge a rule. Don't let them learn that the way to change a maximum highway speed is to constantly exceed it. Being asked to be quiet is not infringing on your freedom of speech since others get a chance to talk. As Matt Delahunty, President of the Atheist Community of Austin says, "My rights end, where yours begin." A great message for kids to learn.
* Unless, of course, the farmer built the henhouse but for this analogy, let's assume a tornado made it from a junkyard ;)