Yes a "Black Flag" which was commonly used to signal no quarters. But a "Jolly Roger" as described by Mr. Dana. There is a difference between the two flags. A "Jolly Roger" flag is most commonly associated with, as Mr. Upton points out, "Pirates", a group of Lawless individuals who plunder and pillage at will. Just exactly the impression that Mr. Dana would be inclined to describe the Seccessionist in his view.
Blacks in Union Uniform were not considered as soldiers by the Southern peoples. But as runaway slaves engaged in rebellion. And as such were subject to summary execution, the same as any Traitor under the law, Black or White. When fighting against Black Union soldier the "Black Flag" was commonly shown for this reason. Here again we are assigning our modern day moralism for their understanding.