Um, hello? Is EVERYBODY here forgetting that part where, in addition to wanting to uproot the Hometree, Colonel Unspellable decides to destroy the very important to the Na'vi Tree of Souls, with the express and explicit purpose of, Quoting the Colonel himself, "Blast[ing] a crater in their racial memory"?
Let's keep in mind that, owing to the Tree of Souls being a major part of the Smurf's USB network, destroying it even if only with TNT would probably have similar effects to, say, dousing the entire Amazon with nerve gas (IIRC, one scientist explicitly cautions the military brass about this possibility) And IIRC the Tree of Souls its self didn't have any Unobtanium
If they had made it explicit that Earth would be dead if they don't get some Unobtanium immediately than maybe the humans would have some more sympathy (Although, as Jello points out the observant types would probably just see Humanity portrayed as the Tyranid Horde). Unfortunately, as it stands, the film's villains look like a bunch of standard-issue money-grubbing Corrupt Corporate Executives who consciously decide to try to annihilate a crucial part of the Smurf's culture (and risk destabilizing the ENTIRE PLANET in the process) because they weren't willing to wait a little longer to get some of those sweet, sweet Money Rocks.
After making someone look that evil, you CANNOT end the film with a monologue designed to make them look good. If you put that monologue in the middle of the film, best before the Colonel launches decides to blow up the Tree of Souls, in order to have a little more moral ambiguity... then it might actually work. But you CAN NOT put it at the end, after the "humanity is full of jerkwads" theme is fully and unquestioningly established established.
(OK, this rant turned out a lot longer than expected. sorry, TL;DR: don't try to make us sympathise with corporate clowns after they consciously try to destroy the native's culture.)