I would imagine that in general the LDS pioneers were far more civilized / educated than the US Native Americans which gave them a far higher likelihood of success than the Native Americans and much easier for the NA's to be exploited.
It was a lot easier for the pioneers to connect with other Americans ( despite being slandered / misrepresented in newspapers of the time ) due to shared language, heritage, etc.
Also it seems like a lot of the land we gave to the Native Americans wasn't land that they could actually do much with. It's not like we gave them fertile farm lands so that they could become farmers. From what little I've learned a lot of the land they got was fairly inhospitable. Whether it's the deserts of the SW or the frozen lands of the Dakotas.