This is not just about hygiene, although if you are really trying to consume everyone else's viruses and bacteria, you couldn't find a better place. Grab that bar or strap to steady yourself and then, once seated, use the same hand to manipulate your sandwich into your germ receptacle (mouth).
It is also not just about the cleanliness of the bus or the metro car, although I am generally grossed out by having to avoid a seat or a patch of floor because of the crumbs — or worse! — that I find there and disgusted by those who would just drop their food wrappers where they stand instead of hanging on to put it in a proper garbage can.
Oh no, this is about the rudeness of it. It is not the appropriate place to eat, just like it is not the appropriate place to have a loud and animated conversation on the phone (but that's a whole other post, now, isn't it?!). You are impinging on the space of others who are using public transit for the purpose it is intended to serve (travel from one point to another) and you are having an inadequate culinary experience on top of that. For shame!
Beyond the bus and the metro, there is another offender I would like to mention that has no place on the sidewalk. This is a relatively new phenomenon, having arisen with the Starbucks and the Second Cups. It is the person stumbling down the street with her/his cup of coffee held out in front at half-arm's length.
This coffee thing tends to happen at all times of the day, but I imagine it to the worst during the morning rush hour. I get it that you are addicted to coffee. I get it that you have some place to be. I get it that you are late. Surely none of these things is well-served by your rude stumbling along the sidewalk with your coffee outstretched before you.
At best, you will have an unsatisfactory coffee experience (probably bad coffee in that cup anyway, getting cold faster than you had planned) and you will arrive at work late and with coffee spills on your outfit. At worst, you will spill your coffee on me and that, my friends, is completely unacceptable!