I try to teach my daughter critical thinking. She is showing herself to be intelligent enough to make up her own mind when she grows up.
I would be interested to read what others do to teach their children about rationalism/atheism/religion etc.
My kido is still really little (3) so I am setting a foundation for making her own choices. I do this by actually telling her "You have a choice, you can 'a' or 'b.' Or is there something else you want to do?" I think it will teach her to think for herself... I hope so at least.
We concentrated on critical thinking processes, observation, and analysis. In other words, we focused on teaching them how to think and not what to think. That sounds good, but it is not easy to keep your opinions out of things. We were rewarded with a brood of four who are quite capable of making rational decisions most of the time. That one of them would wind up being a born again christian was something of a surprise, but a 3 out of 4 true success rate isn't bad. Don't get me wrong, the one who opted for the religious road was not a failure, she just made a decision that was unexpected. Still her decision, and that's fine.
I had my 10 year old son read a kids version of the bible, and asked him to identify the parts he believed and the parts he did not believe. He immediately picked up on the "Universe was created in 6 days" nonsense, and "The Star of Bethlehem" nonsense. As he gets older, and learns more about science, he will likely identify more and more ridiculous things in the Bible.