I can't find the article now, but an evolutionary-psychology noticed that the "cooties" concept seems to exist across all cultures (though obviously not always given the name "cooties"), and furthermore noticed that children often don't consider their siblings to have cooties. I.e. boys will feel that most girls have cooties, but not their sisters.

The psychologist offered this as an explanation: We evolved to find the people we grow up with to be not sexually attractive. This is a mechanism to avoid incest (which can result in genetic problems). However, if you live in a society, you don't want to find people who grow up with you, but who do not share genes with you, to be sexually unattractive (or else you might find no one within your whole society attractive), and thus this "cooties" sensation was placed by evolution so that we can avoid people of the opposite sex during this critical period so that later on, as adults, we may be sexually attracted to them.