During that part of the battle, party members who've you maxed a S link with won't attack you, they'll just stand there and the text will read (character) is hesitating. Apparantly that's what Naoto's doing.
At least I think so. In my playthroughs Yosuke (who's always maxed by then) always hesitates and Teddie (who will never be maxed during that fight as his S link is automatic on certain days) never does.
D'awwwww. But anyways, by then i had my party's s-links maxed, and they brought down hell-fury on me, and Yukiko wasted all her SP on Agidyne-ing me. Maybe you're just lucky.