My reasons:
It was an inexplicable amount of time for Rhaegar and Lyanna not to come back to Kings Landind or another (safer, but still public) place and try to ease the tensions. Lyanna was fierce and loyal and a fighter, so she could not just have left everything go as it might. It was time for her to hear about her brother being held captive (and try to save him), about Brandon and Rickard dying and Eddard being hunted, about Arryn choosing to rebel. It is very much inconsistent with her character. So maybe she wasn't allowed to go anywhere? And to add to this point, maybe Rhaegar did not trust anyone else with guarding her properly and stuck around himself not going back to the KL for this very reason? He was obsessed with the prophecy and had to have her secure.
Another one is Eddard's dream/memory about her pleading with him to save Jon (as we all assume). No matter what had happened, she should have known that he would not harm a child she had with a man she loved. So maybe she was fearing Eddard would not care for the life of the child born when his sister was taken against her will.
I have picked up on the clues that Lyanna might have found Rhaegar interesting when they first met, maybe they had a good moment when he found her out as a Knight of a Laughing Tree. Maybe Rhaegar read more than there was into it and really kidnapped her. Or maybe she even went off with him, but later was held against her will.
What do you say?









