While I don't think there is evidence for the soul's existence as some sort of conscious entity which is apart from the brain or body, I do think the word has its place (perhaps along with 'heart') to represent the very core of our thoughts and emotions, the part of us from which which good arises, the part which Loves, the part which longs for a better world,  the part which is upset and angered by injustice etc.   

There is something important about referring to these important human characteristics with a sort of reverence - I have no problem calling this the 'God' part which is in every human, it seems appropriate and accurately expressive to use language in this way.