User blog comment:The.Outsider/Connor's Father/@comment-1824113-20120831225553

Remember that 'Connor Kenway' isn't his real name. Ratonhnhaketon is. Connor Kenway is the name he adopted so he could move around the cities without people tripping up on his real name.

My money is that Ratonhn (I'll just call them that for now) needed a new name, so Haytham (most likely his mentor as opposed to father) allowed him to take his surname for conveinience sake, or because they had a father-son relationship.