Well, Word of Nintendo is that because of Link going back in time at the end of OOT, the Legend of Zelda timeline was forked at that point.
Nintendo is still pretty screwy about how, exactly, the timeline works out, but from what I understand, Wind Waker and the games that come after (Phantom Hourglass and Spirit Tracks) came from the first timeline, where Ganondorf was banished and Link disappeared because he was sent back in time and thus ceased to exist in that one. Because there was no more Link, when Ganondorf escaped, there was no choice but for the goddesses to flood Hyrule.
The second timeline is the one that started when Zelda sent Link back in time, to the point which we see him at just before the credits roll. We don't see exactly what happens to Ganondorf there, but apparently it paves the way for Link to leave for Terminia and, later, the events of Twilight Princess.
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Nintendo is still pretty screwy about how, exactly, the timeline works out, but from what I understand, Wind Waker and the games that come after (Phantom Hourglass and Spirit Tracks) came from the first timeline, where Ganondorf was banished and Link disappeared because he was sent back in time and thus ceased to exist in that one. Because there was no more Link, when Ganondorf escaped, there was no choice but for the goddesses to flood Hyrule.
The second timeline is the one that started when Zelda sent Link back in time, to the point which we see him at just before the credits roll. We don't see exactly what happens to Ganondorf there, but apparently it paves the way for Link to leave for Terminia and, later, the events of Twilight Princess.