One reason could be the pressure on Boruto. In fanfiction, if Boruto fails to meet the high expectations set by Naruto's legacy, Naruto might show disappointment which could be misinterpreted as hatred. Also, there could be external forces in the fanfic world, like an enemy influencing their relationship, making Naruto seem like he hates Boruto.
It could be that the fanfiction simply doesn't meet Boruto's standards for what the Naruto universe should be like. He has grown up in that world and has his own ideas about how things should be. Fanfiction can be very hit - or - miss in terms of quality and faithfulness to the source material. If it's of poor quality or changes things too much, Boruto might hate it.
It could lead to a shift in the types of fanfiction created. Fans might start to be more cautious about what they write to avoid the idea of Boruto hating it. This could result in less creative and more restricted fanfiction, as people are trying to adhere to what they think Boruto would approve of. On the other hand, some fans might rebel and create even more out - there fanfiction just to make a point.
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.
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.
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.
Sasuke is very likely to be involved. He has a close relationship with Naruto and is also an important figure in Boruto's life. His skills and knowledge could be crucial in any adventure or situation that Naruto and Boruto find themselves in. Another character could be Hinata. As Naruto's wife, she would surely be concerned about any strange events involving Naruto. And for Boruto, she is his mother, so she would play a role in any family - related or village - threatening situations.