His father is the mad king's son - Dany's brother -- so Jon Snow is really her nephew. In their kingdom, that is not a problem so he could end up as her husband after they conquer their enemies. And while the "official" story that Ned told was that his sister was kidnapped and raped, the fact that she made Ned promise to protect her son indicates that the kidnap and rape claim was a ruse.
You all are forgetting an important bit of history. Why was Ned Stark killed?