Jefferson Davis had been a military hero in the Mexican War and Secretary of War for President Franklin Pierce. Davis thought of himself as a military leader and issued orders under the signature of the Secretary of War.
Knowing he wasn't a military man and having no prior experience to rival Davis, President Lincoln took a much more modest role as Commander-in-Chief. He deferred to men like McClellan and the advice of others, something Davis never did.
You may feel otherwise, but IMHO the Confederacy had an excellent chance to win its independence on the battlefield. One strong factor in Confederate defeat was Jefferson Davis playing the role of commander-in-chief. For example, Bragg's lieutenants repeatedly asked for someone else to lead the Army of Tennessee. General Johnston briefly led it during Bragg's absence in the late winter of 1863. What might have happened if Johnston had taken command in March 1863? Better yet, what might have happened if Davis would have listened to advice of competent military men; for example, Robert E. Lee?