Lincoln was assassinated after the fall of Richmond and the surrender of Lee at Appomattox Courthouse. Though there were still a large number of Confederate soldiers under arms, most of the top generals were dead or captured (and paroled), and Southern morale was essentially shot due to a combination of the shock of Lee's defeat and the general depredations of a long and nasty war fought largely on their soil. Joseph Johnston had a large army still in North Carolina (which Lee had been fighting to join before Grant cut him off at Appomattox), but he lacked the stomach to fight on, and surrendered to Sherman.

Basically the Union had captured Richmond, Atlanta, and New Orleans, among other Southern cities. There wasn't much hope left, even though Andrew Johnson, a Southerner, might have been expected to be somewhat more lenient.

Where Lincoln's assassination had more effect was during Reconstruction. If you're interested in that subject the leading authority is the historican Eric Foner, whose book Reconstruction is highly recommended. In brief, Lincoln seemed in the beginning months of 1865 to be considering a relatively lenient process of bringing the former Confederate states back into the Union, a policy that Johnson continued. Johnson lacked the force of character and goodwill garnered by Lincoln, however, and was often at odds with the Northern "Radical" Republican-dominated Congress. Congress eventually overrode his vetoes of their harsher, military-backed reconstruction process, leading to a brief period where the U.S. Army backed Southern governments that ratified the 13th, 14th, and 15th Amendments and, until the Great Compromise of 1877, allowed a relative degree of political and economic freedom for newly freed and enfranchised African American men. After 1877 military reconstruction ended, and the era of Jim Crow, along with the wholesale de jure disenfranchisement of most of the Black population in the South, began.