I look at this movie, and I feel rather let down already from what I've seen so far. The trailers are supposed to give you an idea of what the movie is about, and who the protagonist and antagonists are. If the trailers are intentionally being deceptive, that's one thing, but there is deception and there is outright lying about the movie. It doesn't help that Godzilla has a deep seated following, and that despite how things appear on the outside, Godzilla is ripe full of underlying themes which fit with the idea of Kaiju as a whole. They epitomize fear, the fears that society faces, and how we as humans deal with those fears. Godzilla represented the fear Japan had over nuclear weapons, in particular, the fear they had towards the Hydrogen bomb and the repercussions of it.
No matter how he's depicted, Godzilla is still a force of nature more than a force of evil or good. It can be redirected, and somewhat controlled, but it is still a danger in it's own right and has no love or hate for humans in general. Most of the fights that occur are between it and other Kaiju, reflecting how it seems to only appear when it feels it's territory is in danger. That may reflect why it exactly fights against other Kaiju, simply two animals that are fighting for the right to claim a set patch of land.
In the end, we're not in a greater position than ants watching two cats bicker over ownership of a field. Sure, we can prove to be annoyances, and even drive off one of the two, but ultimately with the Kaiju being a continuous threat in the franchise, we simply choose the lesser of two evils to piggyback on. Godzilla helps keep things in our favor, and he is predictable in his own right. If we removed him as a threat, and destroy him, it will create a void that another will try to lay claim on.