In short, flying is better when you go wide (lots of small creatures) while trample is better when you go big (a few big creatures).
I'd say going big in general pays off better than going wide. Decks that rely on lots of small creatures normally play aggro, which isn't fast enough to win against combo and can easily run out of gas against control. Decks that rely on few big creatures, on the other hand, tend to play midrange, which has a fair match-up against more archetypes.
Moreover, on an average-sized creature, I'd prefer flying because it's harder for the opponent to trade on block, while I can still do so when he's attacking me.
In the end, I'd say flying is better.