Why does Godzilla ?... ( SPOILER)

i think its because the mutos were incedibly agressive kind of how snakehead fish. they kill every fish in there ecosystem and then move on when theres no food is available. godzilla sensing there return decided for the good of himself to attack the mutos and destroyed them so they cant ravage his habitat anymore

actually in the movie he wasn't hunting the muto's, he knew they were back, and he had to stop them from breeding and taking over the earth. :)

I remember dr.serizawa saying godzilla heard the muto's talking to each other and that he was going to restore the balance. :)

Godzilla is an apex predator so it could be because of territory. Alums razor.

Or he thought he would look really badass if he just popped up and ripped their ugly mugs off!  But you know, there could be a more scientific approach too....!! :)

Ok my answer is HEAVILY spoiler filled so be warned if you haven't seen it.

Thay being said there are several parts to this answer. The first is that this species has, according to the interviews I've seen, been around as long as Godzilla. The MUTO can multiply very quickly and cause a lot of damage to the earth and the Godzilla's evolved as natures way to keep the MUTOs in check.  That's part of it, it's his instinct. 

Now, if you look at the part with the skeleton, that was not a Muto skeleton- the spinal column was all wrong for that creature- it was the skeleton of an ancient Godzilla. Where was the Muto's eggs laid? In that old Godzilla. This entails that once the earth became less radioactive and the creatures, Godzilla and Mutos alike, were driven underground, the Mutos had to find different sources of radiation to feed their young. My guess is that the Mutos started fighting and killing their alpha predators, Godzilla, and using the carcasses of the Godzilla's as a location to hatch eggs, at least male ones, which would explain why the egg sacs were there. This would further explain why Godzilla was so intent on fighting and killing the Mutos- self preservation. Should the next have hatched in SF in the movie, Godzillla would have been vastly outnumbered by a species that just two of almost killed him. 

Anyways that's my theory

spoiler ahead be warned as well.

M.U.T.O. means massive unidentified terrestrial organism. meaning from outer space. :)

You mean from earth?....oh by the way LINKMAN89 that skeleton is neither godzilla or a muto, it is something called shinomura I think, they are a type of muto but they were the first to emerge after the Hiroshima bombing and are different to the ones in the film!

Evolving to protect nature is in a way what an Apex predator does, it thins out the herds to keep over population down. Godzilla hunts because thats what an apex predator does.