How can Banquo's children rule Scotland when Malcolm is already ruling it?

Your question references one of the prophecies made by the witches in Act I, Scene 3 of Macbeth. After foreseeing a great future for Macbeth, the witches say to Banquo, "Thou shalt get kings, though thou be none" [I.iii.66]. Yet, as you point out, when the play ends it is Malcolm who is king—and we know almost nothing about what happened to Banquo's son Fleance after he survived the assassination attempt that killed Banquo. So, what gives?

To understand that, we have to look first at Shakespeare's source for the play and second at the political context in which the play was written.

Shakespeare took much of the story of Macbeth from a historical narrative called Chronicles by Raphael Holinshed. In his history of Scotland in that work, Holinshed writes about a historical figure who would become the Banquo of Shakespeare's play, though no mention is made of Banquo's kids becoming kings.

So why did Shakespeare include all that stuff? Well, when Shakespeare wrote Macbeth, King James I was on the English throne. James was also king of Scotland, and he just so happened to trace his lineage (and, partly, his claim to the throne) back to—yup, the historical Banquo.

When Macbeth was originally performed (probably at court before King James I, who was also a lover of all things witch-related) and the line about Banquo's kids becoming kings was spoken, everyone knew who Shakespeare was winking at: the very guy who was sitting on the throne and who paid Shakespeare's salary. That's why the witches prophesy Banquo's kids will become kings—and why Shakespeare didn't need to explain what he meant by that line: everyone in the audience knew it was a reference to their king.

(For a real treat, with all this info about James I in mind, go and look at the image of Banquo's sons that the witches show Macbeth in Act IV, Scene 1 [lines 110 - 123]. Here, again, Shakespeare is paying homage to his benefactor, King James I: "the two-fold balls" Macbeth sees in the kings' hands represent England and Scotland and the "treble [or triple] scepters" stand for James having rule over England, Scotland, and Ireland.)