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I would bet that the people of the time saw themselves as very civilized for not simply wiping the native population out.
Like, when the Mongols sacked Baghdad just 250 years before the European ships started arriving in the Americas: "Most of the residents were massacred during and after the siege, with civilian casualty figures ranging in the hundreds of thousands." The end of the Mongol period was when Timur / Timurlane resulting in the deaths of 20 million people. That's just a century before the Europeans started conquering the new world.
Maybe the Europeans of the 1500s to 1800s thought of themselves as kind and enlightened in that they made treaties with the natives instead of just massacring them. Maybe they thought of themselves as exceptionally kind because they actually assigned land to the natives, instead of simply taking all the land for themselves.
Instead of thinking of the European colonial forces as an especially brutal and rapacious group, maybe it's better to think of that entire time period as brutal.
Also, as an aside, the natives are always portrayed as being peaceful, gentle people who are victims of the awful Europeans. But, we know that they were fighting amongst themselves before the Europeans arrived. The Europeans found native villages surrounded by palisades. There were already native groups who had been driven off their land by other native groups. They were massacred, but that was more a function of diseases and technology, rather than a difference in character.
In the Spanish empire IIRC they were all given citicenship, so yes it could have been handled better, even in that era. In fact, the latino ethnicity is the result of the mix between the natives and the colonizers, which happened because they were integrated.
Thanks, can you provide a source for that? Was that true for indiginous people in the Spanish colonies in the Americas in the 16th and 17th century already? Cause these people were not better off. Spain's colonial rule was as brutal and genocidal as any other. The common whitewashing myth goes that the indigenous population of South America 'was reduced' to large parts in this era due to not being immunologicaly prepared to the 'flu'. Well, they were not 'immunologically' prepared to the metal swords and armour and the bullets of the conquistadores. Many of those who survived were killed by working themselves to death in the forced labour system in notorious Spanish silver mines (see e.g. Potosí). Let's be careful not to portray Spanish colonialism as being something 'civilized'* by the omission of this, but maybe that wasn't your intention.
*Well maybe it was civilized, depending on your view on civilization.
I recommend reading this section of the "Spanish colonization of the Americas" Wikipedia article, which has plenty of sources. Obviously they weren't saints, but, at the time, they were "the dawn of human rights" (cited in the article) and took Christian values very seriously, which is also why they converted all the population forcefully. There's no denying that, but, as a silver lining, education and religion were almost one and the same, and they did build many universities, schools, etc.
When I visited the United States, they always tried to paint it as "they were all equally bad" when it came to colonizers in the museums I went to. However, I feel like that is because the "situation" with natives was way worse in North America than it was in South America.