With the original shuffle, I get it (with the lanyard accessory and so on). I've never really understood it beyond that. But I live fine with my Nano (2G) being this way.... you have to make some small adjustments, like if you put it in your pocket, you should put it in upside down (so that the jack doesn't mash against the pocket bottom).
But yeah.... I'd guess there's some other reason behind it, engineering-wise. The jack was a fairly common failure point on older iPods, wasn't it (my 3G fullsize is fine, but I seem to remember there were lots of people who had the jack go bad). Maybe that has something to do with it.