If you take "God" out of the equation that Jefferson uses (i.e. atheists), on what basis do men have "rights?" 

But the question here is: if an atheist doesn't believe in gods, then whom does he/she believes in? Who are their creators according to them, if its not the 'god'?

The answer is simple. They believe in humans. They believe in Humanity as their religion.

Atheist is a person who doesn't believe in existence of a God. He/she denies the presence of a superior power or deity. But the question here is: if an atheist doesn't believe in gods, then whom does he/she believes in? Who are their creators according to them, if its not the 'god'?

The answer is simple. They believe in humans. They believe in Humanity as their religion. They believe its not the god who created them, its their own parents who made them. For some of them, their parents might be their gods.

So in the context of Thomas Jefferson's speech during the Independence of the US, an atheist, may earn or inherit the 'rights' from their creators i.e. their parents.