From a long article about Larry Hama's first run on the series:
This is exactly where Cobra enters the picture. The series' enemy organization is the expected grab-bag of disposable troops, colorful mercenaries and mad scientists. But, in a rather unique touch for the period, Cobra isn’t portrayed as a threat from without, but from within. Cobra Commander’s slowly-dripped origin story is that of a former used-car salesman who makes his fortune through pyramid schemes and direct marketing. Twice we see his forces taking over small towns in America by essentially promising the dissatisfied citizens everything they want to hear - lots of money, under the table with no government interference, and the ability to keep their lifestyle as-is. A true child of the 1980s political structure, Cobra offers the American Dream to people who consider themselves ‘Real Americans’ - which necessarily involves the creation of ‘unreal Americans’ as counterbalance.
The unspoken fact is that G.I. Joe is the sort of multi-ethnic, multi-racial team that would probably warrant angry four-hour rants on YouTube if debuted today,6 while Cobra seems to be almost entirely white. This notion is made extremely creepy by the recurring ‘Fred series’ - a group of Cobra agents given plastic surgery to appear as generic yuppies, the sort of men America is assumed to trust inherently. More dangerous than the blue-clad soldiers with their guns and bombs, the Freds are expected to worm their way into politics, local and national, to slowly take control of the public perception; to shift the Overton window. And so, the ongoing question throughout much of the series: who is the Real American? The sad answer is that Cobra has as much (or even more) claim to the soul of the nation than the G.I. Joe team.