My two cents
As long as all the episodes are included on the season collections, I personally don't have a problem with what's on the cover. While I can understand the disappointment that one's favorite character isn't on the cover, I barely even glanced at my dvd covers. I was more interested in what was on the discs.
I don't think there's a malicious conspiracy to ignore Mokey, it's probably just that other characters sell better because people relate to their personalities more, so there's involuntarily more of a focus on them. Gobo and Red are the agressive go-getters, Boober is sort of the emo "the world will end tomorrow" type, Wembley is confused all the time, and Mokey is the thoughtful, introspective type who thinks things out and cares about others. Intellectual, spiritual characters have never been particularly popular, and Mokey's arguably the smartest, most spiritual of the Fraggle Five.
I genuinely believe this world would have to be a very different place for Mokey to be hugely popular. . . .