At the end of Godzilla: King Of The Monsters, Dr. Rick Stanton comments that he is glad that Godzilla is on their side and Dr. Ilene Chen adds to his comment with, "...for now." This brings into question whether this is a hint to Godzilla being the villain in Godzilla vs Kong.
While Godzilla has shown to be more benevolent he has shown that he has no problems attacking people. However, most of his attacks towards people is indirect. The humans are more like obstacles for him that he tries to avoid having conflicts with. For instance, in the 2014 movie after Godzilla arrived at San Fransisco the military open fires on Godzilla while he rises out of the water. In order for him to escape, he destroys the Golden Gate Bridge and continues marching towards the MUTOs. The other times the Godzilla has indirectly attacked humans was during his battles with the monsters he hunts for. This can be from him shoving or pushing another monster into a building during the fight.
There was one time where Godzilla has made a threat directly at the humans. In Godzilla: King Of The Monsters, Godzilla first appears when he is swimming and circling around MONARCH's main base of operations, Castle Bravo. He would slam into the side of the base to grab their attention and he would hit harder when the G-Team aimed their guns on him. Lastly, after standing down and opening the blast shields to let Godzilla look inside we see Godzilla's dorsal fins flickering as a display of intimidation.
Back in March while Godzilla vs Kong was still in production, there was a leaked video of the filming at Brisbane, Australia. The video shows a few military troops on the top floor of a garage and a split second before they started firing their guns one of them faintly shout, "It's Godzilla!" I am not saying this is definite proof that Godzilla will fight the military. Perhaps Godzilla will run away to avoid conflict like he usually does. Godzilla has had many chances to make direct attacks at the military when the military attacked first and all of those times he decided to avoid that conflict. I just think now he is going to be pushed to his limit out of frustration. He has shown mercy so many times and has fought to do right in protecting all life on the planet and he still gets attacked for doing his job. So we might actually see Godzilla have a fight with the military.
I have explained in my last speculation post about how Godzilla and Kong will meet for the first time that while Godzilla and Kong are both benevolent creatures, Kong is the one that is more aggressive. In Kong: Skull Island, Kong has shown to be capable of attacking a whole military fleet with just his brute strength when he first appears. The movie even implies that Kong even ate a person before cutting away from the action for a couple of seconds. We also learn though that Kong attacks only those that pose a threat to his home. He has shown tenderness and mercy towards those that are gentle and kind. Yet, his hot-headed personality does get the better of him when he was lured into a trap set up by Colonel Packard and his squad. Thanks to James Conrad's interference, it gave Kong enough time to recover yet Packard's actions allowed "the big one" to rise. Because of Packard's arrogance it led to him being killed by Kong's hand.