The South had many advantages over the North, including more and better military leaders and better equipment in the beginning. They also had free labor at home in the form of slaves so that they could go to war without worrying about their farms.
Many people thought that the South should have won the Civil War despite its outcome. Most of the war happened in the South, so these men were defending their homes from damage. In addition, they were defending their way of life because many were large cotton farmers that required slaves to get the work completed.
Secondly, many of the participants were better prepared than those on the Northern side. Many had fought in the Mexican-American War and already had learned the basics of military conflict. They were also better equipped, having gotten their reward from Mexican American troops that they had killed or taken hostage.