“What are you people fighting for?” I inquired of one of twelve rebel deserters who came into our lines to-day (at Chattanooga). “I could never get to know exactly, said he, but some of our officers tell us we are fighting for liberty.” “Then pray tell me,” said I, “how much of this liberty you have secured for yourself, personally, and what is the nature of it?”
“Liberty,” said the rebel after pausing for a moment, “to enter the Army or else be shot in my own house; liberty to leave my family to starve for the necessaries of life; liberty to fight against my own countrymen, and peril my life to gratify a few slaveholders who are leading us to destruction. I am sick of it and have deserted, and thousands more would do so if the opportunity presented itself.” 
Civil War-era newspapers were organs for propaganda as a rule. While you can’t believe everything you read in a Yankee newspaper this does not seem to be that far off point. Certainly desertion was a problem for the Confederate Army as the war went on, especially in Tennessee. The reasons are probably as complex and different as there were men who elected to take the “French Leave.” However, certain broad patterns do emerge and the question remains as to why so many of the common foot soldiers quit fighting so long before the Generals did?
Many blame desertions on the early institution of a military draft as the primary reason. Technically the Confederate Government did not have a draft, instead they had conscription which is not exactly the same thing. From the soldier’s perspective, it still meant they were compelled to serve whether they wanted to do so or not. Desertion also may not accurately describe the actual purpose of the departure. Many men were away for legitimate reasons, it just appears that for those men who changed branch of service from Infantry to Cavalry might find themselves listed as deserters from their original unit. Southern soldiers seem to have had an independent streak and many held a peculiar notion that whichever unit, regiment or even branch of service should be more or less a matter of their personal preferences. Other men who joined “bushwhackers” or Guerrilla units which were nearer to the home front.
The same Southern women on the home front who were so gung-ho to send the men off to fight wrote letters during the war that the family farm could not be managed in their absence, especially since most were without the benefits of slave labor which the large Virginia plantations enjoyed. In addition some complained that they feared for their own safety due to bands of armed stragglers who claimed any entertainment or convenience available as their right. It was more of a problem than might be imagined. Robert E. Lee wrote in 1862 of the problem of desertion, “I have taken every means in my power to prevent this evil but it has increased rather than diminished.” 
As far as the common Southern soldier fighting for the continuation of slavery, one does not need to dig very deeply to find the resentment in the Confederate rank and file caused by this perception:
“Last night I talked awhile to those men who came in day before yesterday from the S.W. part of the state about 120 miles distant. Many of them wish Slavery abolished & slaves out of the country as they said it was the cause of the War, and the curse of our Country & the foe of the body of the people–the poor whites. They knew the slave masters got up the war expressly in the interests of the institution, & with no real cause from the Government of the North.” 
Maybe or maybe not. Others who deserted did so because they joined the Confederate Army to defend their homes, or put another way “…all the good God gives one man to fight for.” However, once the Army of Northern Virginia left Southern soil and crossed over into Maryland in September 1862 or Pennsylvania in late June 1863, the issue of loss of strength due to stragglers and desertion became serious. Post-Gettysburg and once back in Virginia on July 26, 1863, Robert E. Lee made the following plea, “…the commanding general calls upon all soldiers to rejoin their respective regiments at once. To remain at home at this, the hour of our country’s greatest need, is unworthy to the manhood of the Southern soldier.” 
Responsibility for desertion was placed squarely on the shoulders of the command structure. A bounty of $30 was offered for every deserter delivered to an officer, and in the Army of Tennessee a furlough of forty days was offered to any enlisted man who aided in the capture and conviction of a deserter in addition to the bounty.  In the Trans-Mississippi, General Holmes offered pardons and amnesty to soldiers during early 1863, which met with some success.
The Union was not exempt from desertions either, it was just that the majority of them were “bounty jumpers” who collected the stipend for enlisting, deserted and then did it all over again. It was also harder for Union soldiers to get all the way back home once deployed behind enemy lines in the Southern states. However, they often did not have to go further than another regiment to re-enlist. Some men made enough money at the practice to buy themselves large farms after the war. The Confederate Army did not pay bounties, and hence they had no bounty jumpers to worry about.
1. A. Bailey, “A Deserter’s Confession”, Philadelphia Press, Dec 3, 1863.
2. This was more common than you might imagine. Because of the dietary deficiencies with Confederate Army rations, often all a chronically ill soldier needed to facilitate a full recovery was an extended furlough home where he was decently and more nutritiously fed.
3. Official Records of the War of Rebellion, Series I, Volume XLIX, part 1, (Washington, DC), 1866, p. 143.
4. Diary of James B. Lockney, 28th Wisconsin Infantry in an entry dated October 29, 1863. In addition, Sgt Marcus Woodcock a Tennessee born soldier who joined the 9th Ky (US) pointed out in his memoirs, “A Southern Boy in Blue” that the men of the 9th whether they were from Kentucky or from Tennessee disliked slave owners before the war started. Woodcock was neither Scots-Irish nor was he from the mountains of East Tennessee as were most of the Unionist Tennessee soldiers. He came from a Central Tennessee middle class family. Many rural “working” men and farmers resented the leisurely life and advantages enjoyed by antebellum Southern slave owners.
5. Official Records of the War of Rebellion, Series I, Volume XXVII, part 3 (Washington DC) 1866, p. 947 and also p. 1040.
6. Official Records of the War of Rebellion, Series I, Volume XLIX part 2 (Washington DC) 1866, p. 1240. In general a furlough was thirty days so this represented an additional ten days off duty.