Individual rights (political rights) do not come from the government, the Gods, or society, any more than the laws of gravity do.
One does not need to believe in God to understand and apply the laws of gravity, and this same policy also applies to grasping rights. The principle of rights is a philosophical/scientific and not a religious principle. The basis of rights — both on metaphysical (the facts that make rights necessary and possible) and epistemological (how one comes to learn) grounds — is not faith, but reason.
Rights are based on the requirements of the individual to live with other individuals in an organized society. They are the objective solution to the political problem of how one should live with others in society.
They are a philosophical (scientific) discovery over a long chain of observation and thinking (see the writings of Hugo, Pufendorf, and Locke), which, contrary to Jefferson’s statement in the Declaration of Independence, is far from self-evident. They only become evident to the self when one has properly grasped their proper philosophical foundation.