America had basically two different colonization systems. The colonization of Latin America was primarily for exploration, extraction,and plantation of spices or valuable tropical products (sugar cane, coffee) and the relationship with the natives varied between the colonies. In the Spanish regions, the natives were used as the primary source of labor not as slaves, but in compulsory regimes such as "encomienda" or "repartimiento", while in Brazil the natives (which were less numerous than those in the Spanish colonies) weren't used as labor to the same extent, with many tribes being converted by the Jesuit Order to work in their settlements instead of being slaves (but still being used ocasionally if the slave trade was affected, like during the Dutch invasion of Pernambuco in 1630).

Now, the colonization of the US and Canada was different, as the primary objective was to inhabitate these lands, as was the case of the Mayflower's pilgrims, with the exception of the southern states of the US, which resembled the colonization of L.A. The colonizers still destroyed most of the natives, but there wasn't as much miscigenation compared to L.A, where the culture developed in the countries was influenced both by the europeans and the natives (and africans in the case of Brazil).

As such, in Anglo-Saxon America, the natives aren't as much part of its culture, because it was mostly molded by the european colonizers and immigrants, while there was more of an culture exchange in Latin America, with a more pronounced miscigenation of the population, as stated in the book "The Master and the Slaves" by Gilberto Freyre

Obviously this is multifaceted and complicated, so I'm just addressing one small aspect of it. The legal idea of the natives place in the two different colonial systems was very different. Part of the Spanish and Portuguese claim to the new world grew out of the Treaty of Tordesillas and was brokered by the Catholic Church. Spain and Portugal were expected to make the native peoples Christians and subjects of the Spanish and Portuguese crown. It obviously didn't stop exploitation of the people, but it started the colonies on a different ideological frame work. They weren't just there to clear land for new colonies, they were expected to convert the local indigenous people and "civilize" them and integrate them into the Spanish and Portuguese kingdoms, and the Catholic church.

France (for a little while) and England weren't part of the Treaty of Tordesillas. England, as a protestant nation didn't even have to pretend to pay attention to the treaty. So when England colonized in the New World the indigenous people weren't seen as potential citizens or subjects of the English crown. The English didn't have to incorporate them into their colonization schemes. And they didn't. The encouraged them to move west when they could or forcibly removed them when they couldn't. Land was negotiated for in war and land sales. But the land sales were between heads of state or their representatives. Not at an individual level and the English and then Americans would only allow indigenous people to sale to their state representative. This had obvious distortions on the market, along with the fact that if you didn't take the deal that was offered the English and Americans would just take it through force and that English/Americans were pretty loosey goosey on who they decided could negotiate on behalf of the natives.

In the US we kind of get this weird explanation of the Louisiana Purchase that we bought all that land from the French. Really what we did from a legal standpoint was buy the options to that land, and to be the sole sovereign power with the right to buy the land from it's current inhabitants. So basically, if the indigenous people wanted to sell the land they could only negotiate with the US, who still had to buy the land from the indigenous people.

There was a push to convert/"civilize" the indigenous people in the English/American sphere, but it was mostly left to individuals and had minimal state involvement. There was no pressure from the archbishop of Canterbury to incorporate the Natives like there was from the Catholic church.

That led to kind of a mental frame work in Spanish and Portuguese areas where the indigenous people were potentially subjects and a source of strength whereas in the English and American context they were thought of as foreign interests whose interests were in opposition to the colonial powers.

This comes from papers by Robert J. Miller who's a professor at Arizona's Sandra Day O'Connor School of Law. He had a book that organized the papers into an overarching look at the differences. You can find out more about his book here: https://www.goodreads.com/book/show/547338.Native_America_Discovered_and_Conquered

There's always more to be said, but in the meantime you can find more information in this thread by u/enygma9753 about the complex relationship between the indigenous peoples of Canada and the imperial colonizing powers of England and France, from the birth of New France, its fall and the British North America era after 1763.

Both England and esp. France relied on native alliances -- both commercial and military -- to pursue the fur trade in Canada and to bolster their meagre forces in their colonies. New France was under almost constant attack by the Iroquois, England and its colonial allies for much of its history. And, as a Catholic nation, France had the additional obligation to evangelize and convert the native peoples in Canada. This continued for some 150 years until the Conquest of Quebec in 1759.

The Royal Proclamation of 1763, created in the aftermath of the Seven Years War (French and Indian War), set out the limits of white settlement in British North America, essentially banning further white migration west of the Appalachians and reserving lands beyond to the Ohio Valley for the natives. This was mostly ignored by the American colonists, who continued to settle the lands. The Proclamation also outlined the duties and responsibilities of the Crown (aka the government acting in the name of the sovereign) in its relationship with the native peoples.

After the American Revolution, this proclamation no longer applied to the United States, but it remained in force in the Canadian colonies. In America, the settlers coveted the native lands for agriculture and in 1830, the Indian Removal Act led to the US Army's forcible removal of natives from the eastern seaboard states to "Indian territory" in reserved lands west of the Mississippi. Thousands died of disease and starvation on this harrowing journey, known in the US as the Trail of Tears. The US also pursued wars of pacification in the 19th century against native peoples in the west who resisted American expansionism.

In Canada, it was more economical to arrange treaties with the natives to cede their lands in exchange for reservations than to wage war on them. Often the terms were unsatisfactory and unequal. (The thread linked above goes into the evolution of such treaties in detail.) Many of these treaties have been challenged in court as null and void because they were negotiated in bad faith.

The Crown often didn't fulfill their obligations and were still bound by its duties under the 1763 Proclamation. Canadian courts to this day have upheld this principle, as the proclamation is still part of Canada's constitution and is considered the 'Magna Carta' of Crown-indigenous relations in Canada.

The most obvious answer which has not already been mentioned is just one word. Mosquitos.

It sounds silly at face value, but when you consider that mosquitos were the primary vector for transmitting malaria and yellow fever, it begins to make a bit more sense. From the time of Prince Henry the Navigator until the development, refinement and widespread distribution of quinine, Europeans in groups fared poorly in tropical climates. This is largely due to these two often fatal diseases. The presence of these diseases and their spreaders was a significant barrier to early settlement in the tropical zone of South and Central America. It is also the reason that European settlements in the tropical zone tended to occur at higher elevation when possible, as the altitude and cooler temperatures diminished the threat of an outbreak. Biting activity in mosquitos is based to some degree on ambient temperature. They do not seek a blood meal beyond a certain temperature threshold, and the higher the elevation, the lower the ambient temperature, the less likely they are to exist let alone feed on a human.

When large groups of Europeans arrived in such an environment, by the middle of the first rainy season, the illness would come. The mortality rate pre modern medicine was quite significant. Yellow Fever killed most of its adult victims, children experienced milder symptoms. For the fortunate survivors of Yellow Fever, the reward was immunity from further infection. But of course, there was still malaria. Good ole recurring malaria killed many, and plagued its survivors with fits long after recovery. Any one of these fits had the potential to become medically serious or fatal.

While the origin and cause of these outbreaks was not widely known during the era of colonization, the results and most affected places were known. Cities like Cartagena, at sea level, had a reputation as being sick places. Contrast that with interior cities like Bogata, at its significant elevation, which did not suffer from such a reputation. This was even true up in North America. Charleston, SC might have become the equal (in terms of population) of Philadelphia, Boston, maybe even New York, but the recurrence of malaria and yellow fever outbreaks in the city proper had wealthier locals literally heading for the hills. Such things did not seem to happen there with such frequency or voracity, and it did not escape their notice. If they had a choice in the matter, people wanted to avoid the sick places.

So this presence of malaria and yellow fever affected the settlement pattern, and the economic outlook of an area. Malarial areas had lower European populations, and tended to rely more on coerced labor from enslaved African or Native peoples. There was inherited resistance for some in these groups, who had lived for generations in areas where malaria and yellow fever were present, but outbreaks and illnesses rare. This was noticed both by European settlers, and the people they held in bondage. When the French army came to Haiti to quell a slave rebellion there, Toussaint Louverture, the rebel leader, knew to bide his time until the rainy season, when illness would sweep through the French.

Malaria and Yellow Fever were in fact the reason that the Spanish Colonies were Spanish Colonies for so long. As the power of Spain declined in Europe, colonial competitors made attempts to seize parts of their overseas empire. The British in particular tried several times... Cartagena (1741), Havana (1762), a few others. And guess what? Mosquitos. That’s what. Winged allies from the jungle ate the large population of non immunes alive. Just like the comparatively few Spanish defenders behind their fabulous fortifications knew they would. The Russians have General Winter, the Tropics have General Buzz.

Most of my answer is based on...

Mosquito Empires: Ecology and War in the Greater Caribbean, 1620–1914 (New Approaches to the Americas) 1st Edition

By JR McNeil