I like what Raven said about how the MS has a similar design on it. I think we can rule out flight a mode of transportation, but the game being about the origins of the royal family as well as the MS sounds very likely.
Just because it's the crest of the royal family, doesn't mean it doesn't represent flight, Link could fly around on some majestic bird and that is why they chose to put a bird in the crest. So it doesn't really make difference.
I was looking at some title art for later Zelda games and I noticed a theme, they all have designs that have to do with a major part of the game. For instance, TP's title art has a combination of a wolf and midna's fused shadow,
WW has the king of red lions boat in it
ST has a train...