Ned made a promise to Lyanna on her deathbed, which I'm assuming is claiming Jon Snow as his son.
and on the show (can't remember if it happened in the book), Ned choked up when Jon asked about his mother and promised to tell him the truth -- but only after he's taken the black so Robert/Cat/everyone wouldn't eventually find out.
They way I see it. If Ned was really his father what's the big deal on telling him who his mother really was?
Ned definitely ain't his daddy. And fukk GRRM if he swerves on that shyt.