I think the short answer to why sex is taboo is because it's complicated.
Terrorism, murder, drug abuse, domestic violence and suicide are all things that you don't want to see happening so it's easy to say to a kid (or anyone): "All these things, they're bad. Don't do them." You'd be right to say that, too. You can't do that when talking about sex. Well, you can, but there's a lot more bias in saying "sex is bad" than in saying "murder is bad."
Talking about sex is essentially a conversation in human interactions, but with lots of complications. You can talk about how it's important for people to respect each other, you can talk about how people have freedom of choice, but there are a lot of things when it comes to one person interacting with another that you have to tackle when talking about sex. You might have to deal with issues of equality and gender roles and, basically, when you talk about sex you're not just talking about sex. You're talking about almost anything and there is so much room for people to have conflicting ideas. Add on to that the fact that sex only becomes personally understandable when you reach puberty (and get all those weird feelings) and that it's a different experience for everyone and you have a really complex topic.