WARNING: The following article contains spoilers from Superman: Son of Kal-El #9, on sale now.
After teaming up to investigate the Rising, Superman and Nightwing faced a disastrous turn for the worse. In Superman: Son of Kal-El #9 (by Tom Taylor, Bruno Redondo, Wade von Grawbadger, Adriano Lucas, and Wes Abbott), one of the Rising members they were interrogating was remotely killed by President Bendix, dying in Jon Kent's arms. This left Jon to blame himself for not picking up on the explosive within the man soon enough.
When Nightwing tried to console him though, he admitted that during his years trapped on Earth-3, he had hoped it would be Nightwing who saved him. This ties back to their first meeting but also hints that Jon may suffer from trauma related to his father thanks to Ultraman.
When the two first met, Jon was not in a good place. After just activating his ability to fly, Jon ended up drifting far away from home, triggering a worldwide search by Superman and the Justice League to find him. It was Batman and Nightwing who located him, but when Jon was frightened by Batman's appearance, Nightwing took the lead, being the kind and reassuring presence Jon needed after worrying he would never find his way back home.
This experience stayed with Jon. From then on, Nightwing was the hero he pictured in his head when he tried to be comforting. Jon wanted to reciprocate that kindness to everyone. So when he was once again lost and separated from his family, he secretly hoped it would be Nightwing who found him. He would spend years in that fiery prison wishing for Dick Grayson to show up and bring him home. Of course, it never happened. While Jon languished for years only a few days went by for Nightwing. So, Jon had to free himself, but he still held up Nightwing as his hero.
Why Nightwing though, instead of his father? Jon missed him of course, but why not hope his father, who would have more experience with his predicament, would come and save him. The answer may lay with who specifically imprisoned Jon: Ultraman of Earth-3.
As the evil version of Clark Kent, Ultraman is the opposite of Superman, being largely disconnected from the people of Earth and viewing himself as superior. He enjoys his power, but it does create a feeling of loneliness he can never escape. When Jon showed up Ultraman saw a kindred spirit, or at the very least, someone similar to him. Someone worth conversing with and dumping his deepest held insecurities onto Jon. The boy essentially became Ultraman's therapist, and Ultraman was the only person Jon could interact with for years.
Due to Ultraman's physical similarities to Clark, it's possible that Jon began to dread his visits and subconsciously began to push away the idea of his father showing up to rescue him because it would mean that Ultraman would be coming again. It's twisted and tragic but makes a lot of sense. Still, even though Jon has suffered trauma from his time away, he still holds onto the kindness that Nightwing gave him and seeks to share it with the world. If he could hold onto that in the midst of all his pain, then Nightwing may have unintentionally helped Jon survive his years as a captive.