I'm an atheist mommy. I was raised in a cult. So obviously, I don't want to do either what my parents did (indoctrinate me into a fear-based religion) OR the opposite side of that coin (indoctrinate my son into atheism). I want a new coin. I want him to make his own choice, and hopefully it's one that leads to a happy, fulfilled, ethical life.
Check out this awesome little video explanation of the difference between influence and indoctrination, and how we can encourage our children to make their own worldview choices, while still letting them know our own.