Because if all the fruit is on the top, it gets eaten first. Think about it:
Since the particles of fruit are large and appear less often in the yogurt, if they're on the top, they'll get almost completely ingested at first. However, on the bottom, it's possible to dig thru to the fruit and get some fruit and yogurt at the same time. And by the time the yogurt is half done, the fruit should be somewhat homogenized with the yogurt and will be good.