I would say it is a holdover from the original Japanese movies where Godzilla is essentially a "protector of Japan (or even earth)" in some movies along with long time Rival/Ally Mothra
They probably just saw that and kinda ran with it, except they didn't realise that Godzilla needs an enemy worthy of him being a hero
But then that isn't always true for the originals as Godzilla has been everything from pure evil to ultimate good to just plain doesn't care and will kill anything
it probably doesn't help that, as you mentioned, the MUTO aren't really the antagonist for that kind of setup as opposed to opponents like King Ghidorah, Space Godzilla, Destroyah, Hedorah or Gigan which in the original Godzilla movies are often portrayed as being pure evils that Godzilla can to protect the world from (as well as the Xilians)
But for the MUTO I think the idea was that they are like the beginning of a plague that would result in the death of everything
So the MUTO take the role that Godzilla played in the original Godzilla movie and they represent the idea that continuus proliferation of Nuclear weapons will result in things going beyond our control and things being wiped out
or I could just be overthinking it and they were just badly thought out monsters for Godzilla to beat up