Robert and Lyanna appeared to have a political betrothal. It’s doubtful that they ever coupled before she ran off with Rhaegar. Targaryen children tend to look alike due to all of the inbreeding between brothers/sisters. Jon’s dark hair comes from his Stark heritage through his mother, Lyanna.
Sure wasn't political on Robert's Side being he called her name while humping Cersei and the first thing he did when he got to Winterfell was visit her tomb. And he is known to be voracious in his sexual appetites so... ya know.
And Apparently the Stark Dark Hair Gene is not that strong:
