The recent detection of the Higgs Boson went a long way toward confirming the Standard Model. It in no way confirmed a Theory of Everything. The idea behind such a theory is that if we truly understood physics, we could have a mathematical understanding that would explain how everything behaves - matter, energy, quantum mechanics, dark matter - the whole universe. In extreme, a "theory of everything" would be able to predict asteroid collisions, forecast the weather, and tell what socks you are going to wear tomorrow.
The Higgs boson doesn't do this. Huge parts of basic physics, like gravity, don't fit in the Standard Model right now. It certainly doesn't hint at omniscience, it doesn't make any arguments for or against the existence of God.
So why do we call it the God Particle? Well, first you need to define "we". The media call the Higgs Boson "the God Particle" because it sounds much more approachable and interesting, so more people read the story. Scientists hate the name! The only time physicists seem to refer to the Higgs as a God Particle is to criticize the media for the moniker. Even the person who coined the term, Leon Lederman never meant to imbue religious significance to the subatomic particle. He called it "The Goddamn Particle" because it was such a huge stumbling block for physics to overcome. An editor insisted of changing the name in his book, which probably resulted in a lot more sales but a ton of misconceptions.
