So excluding all photographs of Confederate prisoners by Northern photographers or studio portraits, there are a number out there taken by Southern photographers of enlisted men in the field.3. Images of Confederate enlisted is almost unheard of. With the exception of ones taken by Northern photographers (i.e. 3 prisoners at Gettysburg) you just don't see them due to lack of photographic supplies in the South. If you did have supplies you would be using it to take a picture of Lee or Jackson, not an enlisted flag bearer.
For example, there are these taken by J. D. Edwards of Confederate troops at Pensacola early in the war:
http://civilwartalk.com/threads/the-9th-mississippi-infantry.94555/
Or these of the 1st Texas Infantry in winter quarters at Dumfries, Virginia:
http://civilwartalk.com/threads/men-of-hoods-texas-brigade.92547/#post-760873
Coppens' Louisiana Zouaves, probably taken in Pensacola, ca. 1861:
http://civilwartalk.com/threads/louisiana-tigers-in-new-orleans-1861.108825/
The Clinch Rifles, Company A of the 5th Georgia Infantry:
http://civilwartalk.com/threads/clinch-rifles.77651/#post-547155