This is from WotC's products page, for Races of Eberron:
"This supplement for the D&D game provides detailed information on the psychology, society, culture, behavior, religion, folklore, and other aspects of the races originally presented in the Eberron Campaign Setting. In addition, Races of Eberron also provides new substitution levels, prestige classes, feats, spells, magic items, equipment, and other options for creating exciting characters ready to explore any campaign world."
I think that those who are playing in an Eberron campaign will probably use this book much more than those using FR, Dragonlance, or another published setting (people using homebrew CS's will probably use this more than latter, but not as much as the former). So while we all know that this is really an Eberron supplement, officially, this is a general D&D supplement for the Races line, hence the standard cover.
My two cents: I like the Eberron covers too, though I don't really mind the standard covers either. As long as they deliver the material promised, It's no big whoop.