In addition to that, Samwell Tarly and Gilly uncovered the fact that Lyanna and Rhaegar were secretly married, making Jon the legitimate heir to the Iron Throne. His real name, by the way, is Aegon Targaryen. ... You've never ben a bastard, you're Aegon Targaryen, true heir to the Iron Throne."

So after the Mad King Aerys, Rhaegar Targaryen was next in line for the throne. Then after Rhaegar, the crown is passed to Rhaegar's eldest son. Since Jon is the only living male descendant of Rhaegar, he is the rightful heir to the throne.