Professional historian here, PhD and all, teaching college. VERY few people in the profession see history, American or otherwise, as you describe it. I often tell my students that humans exist in time, and whatever is a part of human experience, is part of history; history = people + time. That's everything, good and bad.
There's some difference of approach, but most professional historians are critical of making their job about moral judgments. The core of the job is to understand what happened and, most importantly, why. I tell my students you could do an analysis of, let's say, Nazi taxation policies and practices, and come away with a completely objective and analytical understanding of how they set up the system, quite apart from the reality that those taxes were intended to pay for the most evil regime of recent history.
But by the same token, we're cautious about choosing "good guys" in history and acting as their cheerleaders. People are more complicated than white hats and black hats. Take someone like Frederick Douglass, for instance; a towering figure in the struggle against slavery, but he also was perfectly willing to thumbs-up the annihilation of Native Americans and threw his suffragette allies under the bus when enfranchisement of blacks was at stake. Most every major figure in history is complex and ambiguous that way, because human beings are that way. And this is equally true of Lincoln or Jefferson (or just about any president) or any other public figure.
To be sure, there's a sector of the profession that does more of what I would call "advocacy scholarship," and they tend to make a lot of noise. Howard Zinn's People's History of the United States (this is the thread about books, after all) kind of charted that path in US history. Zinn was writing around the time of the Vietnam War, when patriotic myths were being used to justify sending young men to die in what he saw as a pointless conflict. A couple of years ago there was an uproar in the American Historical Association when its president wrote an article advocating for the value of disinterested scholarship, not harnessed to current controversies. There was a lot of backlash, but I suspect most practicing historians thought he had a point.
The fact is, people become historians because we love the past - not that we wish we lived in it, but because as we got to "know" these long-dead people and learned their stories, we came to love them, in a sense. We want other people to know them and love them as we do. But when we see people try to turn them into paragons and heroes, for patriotism or some moral crusade or whatever other cause, we cringe; because those moralizing cutouts aren't really them, and they often imply justifying the harm that their darker sides may have caused towards others of their time.
To go back to your post, it isn't that the US (or anything else) exists only because of the various atrocities you mention. But it also didn't come to exist without those things. They are part of the story, alongside the admirable aspirations and achievements. And so we try to tell the whole story, as fully as we can, within the parameters of the page count of a book, classroom time in a semester, and the capacity and curiosity of the student.
