This is indeed a bit confusing to a modern audience. We expect to see all the prophecies come true within the course of the play in order to be sure the witches were right, whereas the implication is that, because all the other prophecies come true before our eyes, we are supposed to trust that the witches were right about Fleance, too. Because Fleance escapes the murderers set upon him in Act III, Scene III, we know that Macbeth has been unable to rule him out of the running, as it were--Fleance is now out somewhere on his own, presumably deciding what to do about the fact that his father has been murdered. Undoubtedly he will want revenge, or at least, will want to be loyal to those who got rid of Macbeth once he knows what has happened. So, we can assume that Fleance makes his way back to the court at some point after the events of the play, even though we don't see him again.
Meanwhile, when Malcolm is made king, the line of succession is restored and the "usurper" dealt with. To an audience very concerned with matters of correct succession, this indicates that the situation has been restored to what it rightfully should be--the play has ended happily. But in medieval Britain, ancestry was only part of what made a successor--a king could also elect to choose a loyal kinsman, especially if he was childless. So it is not that difficult to assume that Malcolm may die young and pass on his kingship to Fleance, if he were to return and declare himself a loyal kinsman, spurred on by the knowledge that Malcolm and his friends avenged Fleance's father.
At the time of writing the play, however, this is not what King James I and VI or his audience would have believed. Fleance was a legendary figure in Scottish history, the supposed ancestor of the Stuart line, whose marriage to a Welsh princess allowed the Stuarts to claim a link with King Arthur as well. Ultimately the sons of Fleance were supposed to have married back into the Scottish line of succession, producing the first Stuart king, Robert II. So this is a little nod to James: look, your ancestor is king right now, so that prophecy was right too.
Most historians now believe Fleance was a fictional character, however, or at least a conflation of various historical figures with bits and pieces of legend, like King Arthur.