There was a very related question asked on AskScience today about why the first words of babies are often double repeated syllables (mama, dada, papa etc), which talks about how for babies still mastering the ability to enunciate syllables the easiest way to say multi-syllable words is to repeat the same syllable twice (re-duplication). As for why it was that particular syllable (ma for mother, pa or da for father), I don't know.. but I suspect the answer has a lot to do with what sounds are easier for babies to make (biologically speaking). Not a very historical answer, but hopefully it is somewhat useful till someone more knowledgeable can answer in more detail.

It's more of a question to /r/asklinguistics because it is related to language acquisition and the build of our speech apparatus. You can read about it here