I think this question underestimates how successful indigenous resistance to European colonization was. Looking back from the 21st century, there is a tendency to condense the history of indigenous-settler relations so that we end up creating an image of inevitable unrelenting European conquest. But that image does not accurately reflect how colonization unfolded. Historians have increasingly come to see European colonization of the Americas as a complicated process that involved a lot of contestation and compromise. This was especially the case in the early stages of colonization, when the numbers of European colonists were limited.

The French were particularly interested in forming alliances with the natives of North America. New France was a colony based around the fur trade and Christian mission work, both activities which required few European colonists and the extensive cooperation of native peoples. As a result, France's native allies were able to exert quite a bit of influence over their European partner. In his book Bonds of Alliance, Brett Rushford has shown how the Algonquin-speaking peoples of the Great Lakes region involved the French in the local slave trade by gifting them captured enemies as slaves. The French, desirous of trade partnerships with these peoples, were thereby inserted into local conflicts and a slave trade which they had very little control over.

In terms of outright resistance, indigenous nations also had success. One of the most well known examples is the Haudenosaunee Confederacy (also known as the Iroquois). Despite suffering from the introduction of European diseases, they effectively navigated the new geopolitical dynamics of European colonization and actually expanded their influence. They exploited the Dutch and English rivalry with France to build trade alliances with them, allowing them to subdue their own rivals and become a major political and military force in the region for well over a century. Their ongoing war with the French was a contributing factor in the slow growth of New France and caused the French Crown to escalate their war with them, ultimately leading to the Treaty of Montreal in 1701. It was only after the Confederacy divided over who to support in the American War of Independence that their power waned.

Even when Europeans appear to have outright conquered Native Americans, things are actually more nuanced when you dig a little deeper. The Spanish Conquest of Mexico for example was largely carried out by native allies, particularly the Tlaxcalans, who used this alliance to maintain favour under the new Spanish regime. I won't say more about that here, but you can check out this answer by u/drylaw about how Tlaxcala was governed following the conquest of the Aztec Empire.

So if negotiation was commonplace and resistance could be successful, why did colonizers succeed in taking over the continent? Warfare between colonists and indigenous nations was frequent and brutal. While indigenous nations could inflict significant damage on European settlements, settler populations, particularly in New England, continued to grow. Over time, the balance of power shifted, especially after France was defeated in the Seven Years War in 1763, removing them as a counterbalance to British expansion. It became increasingly difficult for small indigenous nations to contest the power of British and then American colonization. Nevertheless, even in the nineteenth century, Americans feared the power of an alliance of Native American nations to challenge westward expansion. The disruption of this alliance was one of the war goals of the United States in the War of 1812, detailed by u/partymoses in this answer.

Because we're talking about such a broad topic, this answer can only give a general picture. I hope it at least have given you a sense of how complex the relations were between colonizers and Native Americans. European settlers were not able to simply conquer indigenous nations and impose their will. It was only over the course of hundreds of years that settler societies came to dominate the continent and indigenous resistance continues to the present day. See the ongoing conflict over a proposed pipeline on the lands of the Wet’suwet’en for just one example. If you would like to look into this topic in more detail, below are some of the materials I cited for this post.

Bailyn, Bernard. The Barbarous Years: The Peopling of British North America: The Conflict of Civilizations, 1600-1675. 1st ed. ed. New York: Alfred A. Knopf, 2012.

Kicza, John E. Resilient Cultures: America's Native Peoples Confront European Colonization, 1500-1800. Edited by Rebecca Horn. 2nd ed. ed. Boston: Pearson, 2013.

Lee, Wayne E., ed. Empires and Indigenes: Intercultural Alliance, Imperial Expansion, and Warfare in the Early Modern World. New York: New York University Press, 2011.

Restall, Matthew. Seven Myths of the Spanish Conquest. New York: Oxford University Press, 2003.

Rushforth, Brett. Bonds of Alliance: Indigenous and Atlantic Slaveries in New France. Edited by Omohundro Institute of Early American History & Culture. Williamsburg, Va.: Published for the Omohundro Institute of Early American History and Culture, 2012.