The Commander came from Jason and I joking around one day, talking about how funny it would be the if the first thing Captain America did after getting "thawed" would be to punch Black Widow in the face. You know, for being a commie spy. That lead to a series of jokes about how Cap would react to other prominent heroes with his Depression-era sensibilities. So when I was putting together the roster of instructors, I told Jason that I wanted a Cap spoof like that but I didn't have a name, and he supplied "The Commander" from another thing he'd written back in the day.
To date the strips with the Commander in them have been the most popular. Apparently you guys really like racism. So expect to see a lot more of him!