To answer this we must first dispel the myth that mask are worn to prevent inhaling polluted air.
In fact, the main reason masks are worn is to protect other people's health, not their own. If a Japanese person has caught a cold, he or she will wear a mask so as no to spread it to others.
Masks are also worn if cold or flu viruses are particularly prevalent. We don't find it strange that doctors or dentists wear masks, so why should it be surprising that in cities as dense as Japan that people take to wear masks? If you have ever taken a rush hour train in Tokyo, you'd know certainly be concerned at the risk of being crushed up against a contagious commuter.
You see the most mask worn from February to June. This is because it is the time cedar trees produce their pollen. Hay fever sufferers take to the mask for protection.
Having said all the above, I still don't like the masks. I understand the reasons for them, but it is such a shame when a beautiful girl, immaculately dressed hides her face behind the mask.
Thankfully a mask that can be worn whilst smoking has yet to be invented.