It was a bad idea to hide in Dorne as well, because if anyone was going to be offended by what Rhaegar did as much as Robert and Ned, it was going to be the Martells. His selfishness cost the lives of Elia and her children.
It wasn't necessarily selfishness. When Aegon, Rhaegar and Elia's second child, was born, he said "The dragon must have three heads." His interpretation of the prophecy demanded a third child, and Elia was too weak to give him one.
It is selfish, he was so obsessed with some prophecy he read in a book and he was so convinced it was about HIM that he set in motion events that destroyed his family. Yes, Aerys was more at fault for over-reacting to Brandon Stark's accusation but Rhaegar had his responsibility.
And Lyanna too for being a double-standard twit. She doesn't love Robert and knows he'll cheat on her, so she runs off with a MARRIED FATHER. Apparently, she doesn't care about adultery as long as she's the one hurting someone else (Elia). As a Northern Woman she wouldn't have had any respect for a Polygamous marriage in the first place.
EDIT: Having seen that feature, I think the show will portray Stannis in a more villainous light for this season so that when we get to the huge battle at the end of S2 we won't feel too bad that the Lannisters are still in power.