Some of the best advice I received about raising children as an atheist parent, came from a fellow ex-Muslim atheist who left a comment to the post below, who has, in fact, done just that: He raised his children to grow up to become rational, enlightened human beings.
I also raised my kids who were being corrupted by religious propaganda. I raised certain questions about the ridiculous concept of heaven and paradise and the kids developed some skepticism against religion. By the time they were in universities all of them turned towards rational philosophy. Now they are married and are free from any religious beliefs.
MORAL: Create doubt in their minds but don’t force anything. They would explore themselves and it would be OK. Give them books of Karen Armstrong and others to read.