A while back I did a couple of posts on the care and feeding of young rationalists. Though it is not new, I recently found a truly excellent post on this topic, in Dale Mcgowan's blog, The Meming of Life. The post details a survey carried out on ordinary citizens of Hitler's Germany, searching for correlations between style of upbringing, and adult moral decisions.
Everyday Germans of the Nazi period are the focus of a fascinating study discussed in the PBB seminars and in the Ethics chapter of Raising Freethinkers. For their book The Altruistic Personality, researchers Samuel and Pearl Oliner conducted over 700 interviews with survivors of Nazi-occupied Europe. Included were both “rescuers” (those who actively rescued victims of persecution) and “non-rescuers” (those who were either passive in the face of the persecution or actively involved in it). The study revealed interesting differences in the upbringing of the two groups — specifically the language and practices that parents used to teach their values.
Non-rescuers were 21 times more likely than rescuers to have been raised in families that emphasized obedience—being given rules that were to be followed without question—while rescuers were over three times more likely than non-rescuers to identify “reasoning” as an element of their moral education. “Explained,” the authors said, is the single most common word used by rescuers in describing their parents’ ways of talking about rules and ethical ideas.
Another thing to have in mind is that in the contemporary culture, qualities such as "open-mindedness," "questioning authority," "free-thinking," etc. are universally hailed as ideals, to the point where implying that someone lacks such qualities is considered a serious insult, and is a frequently employed tactic for character assassination. Thus, people endeavor to obtain recognition from others that they have such qualities, and get angry when someone suggests otherwise.
However, like any human culture, ours also has its strong taboos and norms that it's unwise to question, let alone flaunt; to them the respectable label of "free-thinking" doesn't apply. So, what gets labeled as "free-thinking" in our culture may be the real thing, but it may also be a cargo-cult imitation thereof, whose real purpose is signaling respectability, not revealing truth, and where tacit agreement exists not to extend skepticism and criticism to truly sacred taboos. Humans being what they are, we would expect to get much more of the latter, and this is indeed what we see. Thus, I'm extremely skeptical of anyone trying to publicly extol his own, or even someone else's "free-thinking" as a virtue.
Moreover, in any society, including ours, it would be extremely unwise -- even if it were possible -- to raise your kids to be out-and-out fearless free-thinkers who will throw themselves against every third-rail taboo and sacred cow they come across. It would ruin their life prospects. The way things seem, however, it's impossible to have that much direct influence on your kids' character anyway, except to the extent that you can control the peer groups they socialize with -- which is another thing that makes me skeptical of the above quoted work.
The extent to which you can control the peer groups your kids socialize with is quite large. Some religious sects, for example, control that socialization very tightly. The wisdom of such an approach is debatable, but it's definitely possible. A hybrid approach might be to influence (rather than strictly control) the peer-selection process and also attempt to immunize your kids to the worst aspects of their peer culture.