Pooh/Frodo is the more adventurous type and Piglet/Samwise is the loyal tag along. Plus think of scenes like Samwise chasing after Frodo as he crosses the river. Pooh would be the one trying to adventure off and the nervous Piglet chasing after. Or Piglet carrying Pooh into Mount Doom.
True, in terms of their personalities, that is probably the better match. But in terms of physical stature, Piglet carrying Pooh up the slopes of Orodruin is a rather silly mental image.