According to the following site, the reason was that he was focusing on what Jesus taught, the pure moral principles. That would match Jefferson's own description of the work, better than a new theology would.
Jefferson Excerpts follow:
"In 1819-1820, Thomas Jefferson set out to produce the "pure moral principles" of Christianity. He literally cut out and pasted verses from Matthew, Mark, Luke and John into an 82-page book. He described his compilation as the "most sublime edifice and benevolent code of morals which had ever been offered to man..."
"Jefferson's so-called "Bible" was the product of his effort to compile "the Laws of Nature and of Nature's God." It was his expression of Christian morality, not his expression of Christian theology, as has often been falsely assumed."
You can believe what you wish Danny. Omitting that Jesus is God would seem to change the New testament drastically.