Spider-Man (Peter Parker) saves Mary Jane and the kids before Green Goblin (Norman Osborne) takes off with him. After a brutal fight, Green Goblin reveals himself to Spider-Man as Norman. While Spider-Man is in shock, Goblin tries to kill Spider-Man one last time, but ends up impaling himself with his glider. Before Goblin dies, he asks Spider-Man not to tell Harry about him being the Green Goblin. The dead body of Norman is taken home by Spider-Man and Harry thinks Spider-Man murdered him. Later at Norman Osborne's funeral, Harry vows to get revenge against Spider-Man, then tells Peter how good of a friend he is. Afterwards, Peter opts not to end up with Mary Jane for fear of her getting hurt and they kiss. Peter wanders off alone as Mary Jane is reminded of the kiss from Spider-Man from earlier.
Answer: Remember that Green Goblin (Norman Osborne) just found out that Peter Parker is Spider-Man. Aunt May's comment about everyone knows he loves Mary-Jane concerns him because he now realizes that Green Goblin might find/kidnap Mary-Jane just to lure Spider-Man into a fight. This is the basis for the whole reason he can't be with her, as he would be potentially putting her in harm's way all the time if they got together.
Jazetopher