The reason I think "Are you going to have children?" is a rude question is twofold. First, it has to do with sex, and asking people you don't know well about their sex lives is just not appropriate unless there's some reason it might be pertinent to you - you're the person's gynecologist, or sex counselor, or you're both part of some group the explicit purpose of which is to talk about your sex lives, or some other odd circumstance. Second, it is a touchy subject for a lot of people. Some people want to have children but are infertile or have medical problems; some people want to have children but their partners don't; some people are wrestling the "children/career/avocation" demon; some people are just sick to death of having to defend their choice not to have children to parents and whoever else. In some cases it's kind of like asking a person who is single and lonely when s/he is going to get married. Well-meaning, but rude nonetheless.

I agree, if you know for certain that a close friend wants children and it's not a touchy subject for him or her, the rule against asking about it can be waived. Generally speaking, because it's not a touchy subject for me, I don't really mind questions unless they are very clearly from someone who should not be asking. But no matter who asks I do feel a sort of protective instinct toward my fiance, because it strikes me as the sort of thing one should not discuss publicly until getting the OK from your partner to talk about it publicly, and it's just never come up between us.