It could have occurred to the Pueblo that the game would have been a medium to share a bastardized version of their history and spread a mockery of their story.
I'm not trying to flame you or anything, but I'm just saying that that's how the Pueblo could have seen it. It might be obvious to us that video games are great for learning, but it might be obvious to them that video games are just another medium for bastardizing native american cultures.
Or maybe indeed as you say they just have no interest in sharing. Who knows.
Is it obvious to us that video games (like this one) are great for learning? It may be good inspiration to go out and learn more. But as a learning tool itself the civilization series is horrible. For European history perhaps it has some credence, but it shoves in the Teutons and Holy Roman Empire and calls them "German", it completely made up a civ called "the celts", mostly taking from ancient Britons and the list goes on.
For the civs like Germany, the formula at least fits for the leader and name; a nation with borders seeking victory through culture, science, diplomacy or warfare. This is completely blown out of the water if you look back passed the long 19th century Europe, and passed the 20th century most of the rest of the world. The fundamental values that define a civilisation are modelled on north-western Europe in the 19th century, particularly victorian england.
For civs like the Aztecs it starts to break down further. For the large part we see them as a "state", but despite applying them like one to this game, the developers didn't actually differentiate between what was aztec and what was not. One of their city names is Tlaxcala: a people never conquered by the Aztecs and in fact in a perpetual state of war with them. Tenochtitlan was abandoned as a city after its days of eminence (before the rise of the aztecs) yet it also made their city list, as did Tiwanaku in the incas despite a similar situation. So even when these principles that do not apply to native american peoples are applied to them, they are not applied properly.
So then to Puebloan people, people who had developed entirely independently of the rest of the world for thousands of years, this just doesn't make sense. And having lost their land and economy, having lost their identity to homogenised ideals of "native americans" in headresses and teepees they then find a company wanting to change their history by treating them with a criteria based on western ideals of civilization and playing them against the rest of the world. On top of that, they are told this is "educational". If i was pueblo, i'm sure i'd be pretty cheesed off if some americans came down here and told me they wanted to play with my culture too.
As much as i love civ v, i can appreciate that as far as history is concerned this game is horrible. The civilopedia provides some saving grace for those who go as far as to browse it, but it's still not great. I'm hoping for Civ 6 they come up with some solutions that don't homogenise world cultures into 1 format of state, but i can understand how difficult this may be, so i can accept compromise for the sake of gameplay.