I don't play Terra because it's not really my thing, but while I can see how it can be viewed as racist, you have to remember that this is a very loose interpretation of history where all the more gruesome and terrible aspects of humanity are reduced to basic gameplay aspects or are not present at all. If you wanted to a South American civilization could conquer the world or become a dominant power, and a European power could get wiped off the map, and it's all done without a speck of blood ever spilled. This game is not a realistic portrayal of actual history, it's a game where you rewrite it to whatever you want it to be, that's all it is.
It's only racist if you perceive it to be, and with the Terra maps, you have to strain perception to make it racist, and even then it's very benign. The terra setting is vaguely evocative of European discovery and conquest of the New World, but the maps do not look like Europe and the Americas, none of the civilizations have to be European, in fact the only real connection is the "All players begin in the Old World" description. Change the description to "all players begin on the same continent", and you probably wouldn't even see the New World/Old World connotation at all.
And basically, barbarians are just another aspect of the game, one that's supposed to do nothing but attack you for a little bit of extra challenge. It's already been said, the barbarians don't represent anyone, they're there so something can directly oppose you in the early game, and with Terra, make it just a little harder for the people settling the new continent. If you don't think of it as "Europe vs. Americas", then it's simply "bunch of civs race to take landmass where some barbarians eventually spawned." I think it would undermine the idea of the Terra map if some actual civilizations were on the other continent because then it'd be a fractal/continent type game, in which case you might as well play one of those settings. Or you can turn the barbarians off. Problem solved.
So, while I can see how it can be viewed as racist, doing so does not mean you're protecting the dignity of Native Americans or that you're a better person for thinking it's racist, like the topic creator strangely thinks. If anything it's more like a "hey, that's kinda racist ha-ha" thing. Then you keep playing, because it's some vaguely insensitive thing they did but isn't worth thinking about beyond the first notice.