You have to wonder if she'd had free choice, would she have picked Robert? Doesn't she express doubts about him to Ned?
Lyanna wouldn't have chosen Robert. An excerpt from GoT:
"Robert will never keep to one bed," Lyanna had told him at Winterfell, on the night long ago when their father had promised her hand to the young Lord of Storm's End. "I hear he has gotten a child on some young girl in the Vale." Ned had held the babe in his arms; he could scarcely deny her, nor would he lie to his sister, but he assured her that what Robert did before their betrothal was of no matter, that he was a good man and true who would love her with all his heart. Lyanna had only smiled. "Love is sweet, dearest Ned, but it cannot change a man's nature."
Clearly this suggests that Lyanna was anything but pleased with her father's choice for her. And Ned, being honorable to a fault, was not about to lie to his sister, but having loyalty to Robert, he opted for "but it will be different when it's you" which is little more than "empty optimism" in the face of glaring evidence to the contrary. (Come on Ned, you held the girl in your arms; are you really going to try to lie to your very assertive she-wolf sister?)
Maybe someone unscrupulous lied about the rape scenario to keep Ned in the game, and to further Robert's rebellion. Robert lies to himself to avoid recognizing that he was rejected, for who he is as a man. {...}He would be furious with Lyanna and feel inadequate(especially since Rhaegar was the better man in a lot of ways) if he allowed the truth to sink in. Also it would make him more of a usurper. Instead she is idealized and made the victim or Rhaegar is villainized. Assuming it was not rape and abduction, of course!
Eulalia, you also raise an excellent point. The only person who refers to what happened with Lyanna as rape is Robert, told to Ned. Robert would need the Starks to press his advantage, and the only way he can hold the honorable Starks in his ploy for destroying all things Targ and claiming the Iron Throne is by making it a matter of honor. If the war is about rescuing Lyanna who has been so grievously wronged, raped, and otherwise abused, the Starks would absolutely have to rally to the aid of their own blood. If it were to be discovered that Lyanna, who had no affection for Robert, ran off with Rhaegar, then Robert's war on the Targs is nothing but petty revenge, something that the Starks would never stand for.
TK-421- I am in absolute full agreement with this statement. Cersei is nothing if not effective in ridding herself of unwanted [things].