Maybe it's the high expectations that Naruto has for Boruto. Naruto is a hero, and he might unknowingly put a lot of pressure on Boruto to follow in his footsteps. Boruto could be scared of not being able to meet those expectations.
They could start by having an honest conversation. Naruto could sit down with Boruto and just listen to his fears without judgment. This would be a first step in building a better relationship.
It could also be due to a misunderstanding. Perhaps there is some misinformation spread about Sasuke in the fanfiction, like false rumors that he has a hidden and malevolent plan. Naruto, being someone who values their friendship deeply, would be scared at the thought of Sasuke turning into an enemy because of these untrue stories.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.
Yes, there are likely to be such fanfictions. In the Naruto series, Sakura can be quite assertive and strong - willed. Her temper and skills could potentially be a source of intimidation for Naruto in the creative interpretations of fanfiction writers.
Physically, Naruto can use his Rasengan or other powerful jutsus to fend off enemies attacking Boruto. His combat skills are top - notch, and he won't hesitate to engage in battle to keep Boruto safe.
One possible reason could be that Naruto had a traumatic experience related to thunder when he was young. Maybe he was alone during a thunderstorm and something really scary happened, like seeing a lightning strike too close for comfort. This could have left a lasting mark on his psyche, making him fear thunder in the fanfiction.
In many Naruto fanfictions, Naruto might have developed some new and unique abilities that the Kyuubi has no defense against. This could make the Kyuubi, which is used to being a dominant and feared force, feel vulnerable. For example, if Naruto has the power to nullify the Kyuubi's chakra or to manipulate it in a way that goes against the Kyuubi's will, it would be a cause for fear.
In the 'boruto kills naruto fanfiction', a motive could be a power struggle. Boruto might believe that Naruto's power is holding back the village's growth or his own potential. He could think that by eliminating Naruto, he can bring about a new era of power in the Hidden Leaf. Also, it could be out of desperation. If Boruto is in a situation where he believes that killing Naruto is the only way to save someone he loves, like his mother or a friend, he might take such a drastic step.