In this interesting article, Lama Yeshe explains some of the common misconceptions and the purpose of mantra in Buddhism. From the article:
It is a common misconception that reciting mantras is an external and unnatural mental exercise, rather than an internal and spontaneous occurrence. Reciting a mantra, however, does not mean the mere vocal repetition of speech syllables. Many meditators know from experience that the act of reciting mantras transcends external sounds and words. It is more like listening to a subtle inner sound that has always inhabited our nervous system.