Wikipedia actually has an interesting interpretation:

Attempts to explain the symbolism of the rite also must negotiate the illogical placement of the coin in the mouth. The Latin term viaticum makes sense of Charon’s obol as “sustenance for the journey,” and it has been suggested that coins replaced offerings of food for the dead in Roman tradition. This dichotomy of food for the living and gold for the dead is a theme in the myth of King Midas, versions of which draw on elements of the Dionysian mysteries. The Phrygian king's famous "golden touch" was a divine gift from Dionysus, but its acceptance separated him from the human world of nourishment and reproduction: both his food and his daughter were transformed by contact with him into immutable, unreciprocal gold. In some versions of the myth, Midas's hard-won insight into the meaning of life and the limitations of earthly wealth is accompanied by conversion to the cult of Dionysus. Having learned his lessons as an initiate into the mysteries, and after ritual immersion in the river Pactolus, Midas forsakes the “bogus eternity” of gold for spiritual rebirth.

Wikipedia also says,

In Latin, Charon's obol sometimes is called a viaticum, or "sustenance for the journey"; the placement of the coin on the mouth has been explained also as a seal to protect the deceased's soul or to prevent it from returning.

The basis for these interpretations are analyses of Latin writers; the theories stem from, among others, "Charon's Obol" by Susan T. Stevens (see below), Money and the Early Greek Mind: Homer, Philosophy, Tragedy, by Richard Seaford, and Modern Greek Folklore and Ancient Greek Religion, by John Cuthbert Lawson. The above quotes are condensations of their work as historians.

I may be reading too much into this, but The Golden Ass, by Apuleius, contains this passage (emphasis mine):

(So even among the dead, greed enjoys its life; even that great god Charon, who gathers taxes for Dis [Haides], does not do anything for nothing. A poor man on the point of death must find his fare, and no one will let him breathe his last until he has his copper ready.) You must allow this squalid elder to take for your fare one of the coins you are to carry, but he must remove it form your mouth with his own hand.

This seems to support the idea that the coin sealed a dead person's mouth, but it could be merely a complete coincidence; "breathe his last" could be used in place of "die".

Charon's Obol and Other Coins in Ancient Funerary Practice, by Susan T. Stevens, gives evidence to support the viaticum-coin-as-sustenance theory, citing Apuleis's usage but as food, not breath. She does mention that other "Latin authors" (unspecified) wrote that the coin was used to seal the mouth to prevent the soul from escaping.

The two main theories, therefore, are