It has to do with this idea that was started by 13 colonies that decided to throw off the yoke of an empire, and said, “We hold these truths to be self-evident, that all men are created equal, that each of us are endowed with certain inalienable rights, that among these are life, liberty and the pursuit of happiness.”
See what is missing from this official White House transcript?
The first time the President edited the Declaration of Independence to omit any reference to God, one could reason that it was a misquote, a slip, or bad copy editing on the TelePromTer.
Not this time. We now accept that the President is intentionally removing the concept of God from his quotes. There is no other explanation, unless he is prone to making the same bizarre mistake twice in the same way in the same context.
This isnt a case of judicious preference: a President who opts to say Bless America, and not God bless America, may draw little real attention, and more than a person who says Happy holidays, as opposed to Merry Christmas.
This however is a specific quote from a specific document. You dont make an edit like this unless it reflects something specific. You can already guess why he is doing it: he does not believe that inalienable rights come from God. They are merely on loan from the government.