There is a consensus in the medical community that Lincoln suffered from Bi-Polar Disorder. The disease is suspected in other presidents throughout history, but generally accepted for Lincoln. Bi-Polar sufferers endure periods of great despondency, despair and depression interrupted by periods of great productivity and generally high spirits. Knowing this, it becomes difficult to get much of a handle on what Lincoln believed (or didn't believe) unless he consistently repeated the same message. The fact that he was constantly dealing with enormous personal, professional, and national tragedy doesn't help matters.
This is, of course, not all of the answer, but part of the answer. Another big part is the fact that almost from the minute Lincoln died "friends" began stepping in to assassinate his character. To this day, you will find thousands of people here on FR who are convinced that this nation's greatest president, a Republican, was a racist and a scoundrel.
Lincoln was a racist by today’s standards...almost everyone was then, even abolitionists.