Because morally, it was. Morally speaking, nearly all wars are seen as wrong, depending on what institution has founded a group's morals.

Native tribes took land from other tribes and had their own territorial conquests before the Europeans arrived, so why is there such a negative perception on the land being 'stolen' from the Native Americans, who had previously stolen it themselves?

Logical fallacy. (Edit) I believe a "No True Scotsman" fallacy Strike that. I was wrong. It would be the "tu quoque" fallacy. /u/Reedstilt made a good analogy once where he said:

I never understood the point of arguments like this. Does the fact that peoples everywhere have had violent conflicts negate their right to defend themselves when peoples from elsewhere invade?

I only ever see arguments like this in the form of "The Aztecs were fighting all the time, so they don't get to complain when the conquistadors come knocking" but never "The English were fighting all the time, so they don't get to complain when the Luftwaffe comes knocking."

One thing people seem to forget about with regards to the colonization of the Americas is that many atrocities occurred after the wars had already ended. By the end of the 19th Century, most wars were over between tribes and the U.S. government. The U.S. then proceeded to violate every treaty they made in some way, shape, or form. This included the theft of millions of acres of land via the Dawes Act in 1887, the massacres of Wounded Knee and Sandy Creek, the neglect of tribal reservations, the abuse of power by Indian agents, the forced sterilizations of Indian women up until the 1970s, the termination of the trust responsibility with tribes in the 50s and 60s that resulted in numerous deaths of tribal citizens due to the lack of healthcare, the forced assimilation of natives in where they were literally taken from their families without a choice and shipped off to boarding schools that could be thousands of miles away and where they were punished for being Indian, and many, many, more wrongs committed.

Why it is often perceived as "wrong" (which is often isn't) is because the U.S. often claims some moral high ground in the world. It acts as the "land of the free and home of the brave," yet it continued to commit these kinds of legal and moral violations well into the 20th Century, a time not too far away in where we can judge something with relatively modern standards without the term "revisionist" being thrown around.

Yes, tribes did wage war with each other and did commit atrocities of their own. However, most people in the world today agree that killing innocent people is wrong just like they did 500 years ago. Tribes believed that within their societies just like those of Europe and those of Africa did. We cannot force a modern interpretation on the past, but we can observe the morality of the past and draw comparisons to our day. The fact that tribes had issues doesn't mean that is justification for third party to come in and do even more wrong.

Moving on to a more historical aspect... Most people were fine with letting the past stay in the past regarding relations with the Indian Tribes. In the 60s and 70s, though, the rise of the Civil Rights movements began to challenge the narrative in the country. Natives also participated in these events and even had a movement of their own created, which is known as the American Indian Movement. Since then, efforts have been made in the field of academia to reexamine the past and identify what exactly has happened. A big author who wrote in issues like these is Vine Deloria, Jr. He is a Native American historian and author who has written many books considering the legal and ideological standings that have shaped the story we now have today. But this topic starts to bleed into many more aspects than just a historical field, so I'll stop it there.

Because of what Europeans powers did, not the fact that they conquered.

A very basic example, here is how Columbus described the Tainos:

"They traded with us and gave us everything they had, with good will ... they took great delight in pleasing us ... They are very gentle and without knowledge of what is evil; nor do they murder or steal...Your highness may believe that in all the world there can be no better people ... They love their neighbours as themselves, and they have the sweetest talk in the world, and are gentle and always laughing."

Suffice to say that what Columbus did to the Tainos after this was the very opposite of this description.

Here is another simple example, taken from South America: the Incan Mit'a.

The Incan administration instituted a labor tax called the Mit'a throughout its empire. Under it, a few men from each administrative unit were required to perform labor for the state. These tasks included building farming terraces, roads, buildings and irrigation, mining, fishing. More dangerous jobs were performed for shorter amount of time, in order to be less burdensome to the taxpayers, and most of the projects benefitted the local communities (by supporting agriculture and infrastructure), and were located close to the homes of the laborers. "The underlying ideology as that of a reciprocal exchange. The state provided for the worker in exchange for the labor the worker gave the state." (The Incas: New Perspectives by Gordon F. McEwan)

When the Spanish conquered the Incan territories, they retained the Mit'a system, with a twist. They vastly increased the amount of menpower conscripted (relative to existing population), especially for mining purposes, and kept them perpetually working in terrible conditions. (There is a reason that Potosí is known as the Mountain that Eats Men). This devastated local communities as they were deprived of manpower for the agricultural season, not to mention the mass deaths due to the labor. This is because system changed from a reciprocal exchange between the laborer and the state, to one where the need to gain revenue far outstripped the welfare of the laborers. To the point where to this day districts that were required to provide mining mit'a still suffer economically despite the system being abolished in 1812.

Here we have two conquering empires, with far different ways of treating their citizenry.

Also consider the Haudenosaunee, who formed as a confederation of 5-6 nations. They, too, also conquered much territory, but they have a very different way of treating the conquered.

"It has been a constant maxim with the Five Nations, to save children and young men of the people they conquer, to adopt them into their own Nation, and to educate them as their own children, without distinction; These young people soon forget their own country and nation and by this policy the Five Nations make up the losses which their nation suffers by the people they lose in war."

They absorbed the conquered into their own society, an welcomed any who wanted to join. This isn't because of altruism, but it created a far more accepting society than the European colonists of the time. This policy was also common among all the natives groups in the region. Compare this to the colonial policy of shipping the defeated off to godforsaken reservations (if not killing them outright) and there is a readily seen difference in the human cost between the two conquests.

Suffice to say that European colonists had far, far bigger problem with viewing the conquered peoples with dignity and caring about their welfare, compared to native conquerors. And the actions of the colonists often horrify modern observers, for good reason.

But even if the Europeans didn't do anything worse than the natives. Why would that matter? Should we not care about the crimes committed by the Soviet and Allied forces in WWII because the Axis were worse? It just seems like a nonsensical question whatever which way.

I'd like to point out that the morality of the colonization was questioned even within the colonial power Spain. The Valladolid debate (1550) was between Sepulveda and Las Casas.

Sepulveda argued that making war on the Indians was just "in order to uproot crimes that offend nature", specifically human sacrifice and cannibalism, and that enslavement was just on the same grounds. He also invoked Aristotle's idea that some peoples were naturally suited to slavery. He also suggested that coercive treatment went hand-in-hand with forced conversion to Christianity.

Las Casas argued that the Indians did not meet Aristotle's definition of the "barbarian"/natural slave; they were capable of rational thought, and should be persuaded peacefully to convert Christianity. Las Casas also said that the brutal treatment of the Indians was inhumane and unjust.

Las Casas is a complex figure himself, who himself owned slaves on an encomienda in Cuba until his epiphany in 1514, divestment, and return to Spain. For a while his argument for ending Indian slavery also advocated replacing it with "acceptable" African slavery. Then he retracted this position. He also advocated for more-sustainable, less-extractive settlement structures, which werent implemented. He has been criticized for giving fodder to Spain's colonial rivals and the "Black Legend" narrative.