There are two leading explanations for why it was called the God particle:
1) It will explain how the universe was created (or at least bring us significantly closer), from a scientific standpoint. Finding it will not disprove the existence of a deity, nor will not finding it prove the existence of one.
2) It was nick-named that as a tongue-in-cheek 'We think this particle is everywhere but nobody has actually seen it.' (this came from an earlier Slashdot article, you can look it up for yourself later)