Note: Spoiler Alert info below...pass this post by if you're in the process of watching GoT and don't have the entire story yet.
Isn't Jon's real dad Dany's brother though? Yes,,,,that would be correct, KL (see explanation below per the lineage. Again...those who are still catching up with the series, avoid reading below as there may be some backstory information you'd prefer to discover on your own).
I was thinking the same thing until another fan informed me I was mistaken about Jon Snow's parentage. The fan needs to go back to GoT University....he/she is mistaken, not you.
Originally Posted by KittyLamour
As we all know now (per last season's finale) Eddard (Ned) Stark's bastard (Jon Snow) is not his child as he claimed all these many years. Jon is the offspring of Ned's sister the She Wolf, Lyanna Stark, and the (former) Crown Prince Rhaegar Targaryen (whom future-king Robert Baratheon killed in battle at Ruby Ford) during the rebellion.
Rhaegar was married (to Elia Targaryen) but had fallen in love with Lyanna (and of course had an affair and subsequently a love child). So when brother, Ned, rescued her post-end-of-the-war, at the Tower of Joy, she had him swear to not reveal Jon's true identity since Robert would obviously have him killed.
And, back to your original question, yes, Rhaegar was Daenyery's eldest brother....making Jon Snow, the "King of The North", her nephew. Not likely they'll hook up come series finale (unless they tend up taking a page from Jaime and Cercei's book).