WHat does it mean?
Regarding the fly imagery in the song, there are no available records of any meaning attributed to it by Bishop, and no body of research devoting any significance to it, either, but an imaginative listener can come up with several potential layers of meaning. Since the song is a product of the Civil War era and Bishop and his men were on the Union side, it is easy to imagine the fly as an embodiment of a slave master, or, since it is a military song, a commanding officer. The lines, “If I sleep in the sun this nigger knows/a fly come sting him on the nose,” make sense in that light. Some versions of the song make references to "Massa Lincoln," Tennessee, etc., so there could be meanings pertinent to the War and the era that modern day listeners won't fully grasp. There could also be Biblical symbology present, with the fly representing Satan. In Revelation, Jesus calls himself the "Bright Morning Star (22:16)," and says he will give the morning star to those who overcome (2:28). In that case, the song could be interpreted as telling Satan to shoo because the singer belongs to “Somebody” who makes him feel like the Morning Star. Lines about angels singing, pouring molasses on the head, and taking wing could be referring to spiritual blessing and eventual deliverance. It could also be that there were a lot of annoying flies in their camps and on the battlefields, and being bothered by flies, by day and by night, was a regular part of their lives, and the catchy song helped make light of it. Finally, Mr. Bishop was a performer; maybe the whole thing was written with a bit of blackface stage humor in mind.