PhotonicBoom is correct in saying that the airflow created by blowing across the top of the coffee will replace the coffee-heated air with cooler air that will absorb more heat from the coffee. It also allows more of the coffee to evaporate (which might seem like a bad thing, but evaporation is simply the hottest molecules becoming gaseous and leaving, so it has the effect of cooling down the coffee) because air can only hold so much water vapor, and it can absorb water vapor more quickly at low humidity levels. By constantly moving the air above the coffee, you are insuring that the humidity will remain low (relatively - your breath is actually fairly humid but still less than the stagnant air above hot coffee).
Blowing into the coffee will cool it more quickly than simply blowing over it because it creates all of the above effects, but it also creates turbulence in the coffee itself, which also cools the coffee. Because the coffee can only evaporate from the top, a majority of the liquid stays pretty well insulated when still, so the only heat transfer from the bottom of the cup to the top is convection, and water has a very high heat capacity so it does not conduct heat very quickly. By blowing into the coffee, you effectively stir the coffee, moving the hottest molecules around so that they all move to the top of the cup and have a chance to escape into the air at some point. The uneven surface also has more surface area than a flat surface, giving even more molecules the chance to escape.
Note: Your breath is actually a pretty poor gas to use to cool down coffee efficiently due to its high temperature and humidity. To maximize efficiency, try to blow from the front of your mouth rather than pushing from your throat. (I don't know how much that makes sense - it's something that musicians are often instructed to do to change their tone. When you blow from the front of your mouth, like you're whistling, the air is cooler and drier than when you breath from the back of your throat, like when you yawn.)