Now that we know Jon is actually Ned’s nephew, the name Jon itself draws a parallel between the two characters in a way that hasn’t been immediately obvious to everyone.
Jon Snow, specifically, is named after former Lord Paramount of the Vale Jon Arryn, who raised Ned in his youth and served as a father figure to both him and Robert Baratheon.
One Game of Thrones fanatic noted on Reddit that all of Ned Stark’s sons are named after people Ned Stark was close to in life, such as Rickon and Bran being named after Ned’s father and brother, respectively.
It’s known that one reason this name was chosen was to keep the non-bastard child safe from Robert, whose hatred for Rhaegar Targaryen could have meant bad things for the child.