Yes, this refers both to Loki’s Frost Giant anscestry, as well as Odin’s plan to someday forge a peace in which Loki would rule over Jotunheim as King of the Frost Giants.
Deano’s answer to: “At the beginning of Thor, why does Odin tell Thor and Loki (as boys): ‘Only one of you can ascend to the throne. But both of you were born to be kings’?”
deano.com 
did you get this from the comics? the movie says nothing of a plan of Odin’s to have Loki rule the frost giants as king, though it does talk about Odin’s plan to use Loki for peace with the frost giants in some way. But it is not specified how
I get it from a combination of Norse myth, as well as the Marvel Comics specific interpretation – in both cases, Loki is half Frost Giant, and (secret) heir to their king. It isn’t spoken aloud, but it’s also pretty easy to draw the link from what transpires in the movie, and Odin’s description/flashback of how he came to adopt Loki.