Putting it at the bottom makes it consistent with the iPod touch. I would argue it also makes more sense since the headphone jack can force you to orient your device in such a way that double clicking the home button to access music controls isn't easy. For example, the headphones are in while your phone is in your pocket. You have to pull the entire device out to change songs, whereas you could expose only the bottom quarter of the screen from your pocket if the jack was on the bottom.
It also makes it less awkward when you have the USB cable and headphone jack in and they're not on competing sides.
Another thing: When you're talking and it's raining, water is less likely to fall in the speaker hole. I'm not sure if this was ever an issue, but it's something I think about when I'm walking the dog and talking when it's misting or raining lightly. I'm sure it's more about maximizing space than anything, but that would be a benefit.