With recent speculations on how Link will travel between Hyrule and Skyloft, there is at least one thing known: Link will not possess the ability to fly. In a recent interview with Eija Aonuma, he confirms that Link will not be able to fly in the upcoming Legend of Zelda.
“[Laughs] I hadn’t thought of that [Epona as a Pegasus]! You surprised me with that one! Of course, you know, Link does have to travel between Skyloft and the land below, and back and forth, so he’s obviously going to have to do that via some sort of conveyance… That being said, I’d like to reveal that at a later time, so I don’t want to give away too much other than to say that he is going to be travelling between the two. However, I can guarantee he’s not going to be flying around like [Pit from] Kid Icarus!”
Which brings up the question, “How will Link get to Hyrule?”. I personally think there will be some sort of flight, but not with Link flying himself. In previous games, such as A Link to the Past and Ocarina of Time, Nintendo liked the idea of Link being carried by a bird. If you remember in A Link to the Past, the flute (ocarina-looking item) summoned a white bird to carry Link to several locations. I believe Skyward Sword will have something similar to this. However, I’m curious to hear your thoughts, so please comment!
Source: Official Nintendo Magazine