I'll start off by saying you may have some additional luck asking some of the other "ask expert" subs, such as /r/asksocialscience, r/askliterarystudies, or r/culturalstudies. Your question lives in the liminal, theoretical space between historiography, education, and cultural studies, so it'd be good to balance a historian's take against an educator's against a cultural studies person, and so on.

That said, here's the take of a former professor of mine, Phil Wegner:

The reason that the tale of John Brown is largely lost in American History education is Ronald Reagan. Bear with me.

Back in 1940, Ronald Reagan co-starred with Errol Flynn in a B-movie western called Santa Fe Trail. This film's antagonist was none other than John Brown, portrayed by the cantankerous old coot, Raymond Massey. In the film, Brown was portrayed as a ne'er-do-well with biblical delusions. All of his actions, from Bloody Kansas to the Raid at Harper's Ferry were shown to be acts of domestic terrorism perpetrated by a religious zealot and his brainwashed followers. In his work-in-progress book, The Battle for John Brown's Body: Representing Radicalism in 20th Century America, Phil Wegner argues this image of John Brown continued throughout the twentieth century, running as a sort of parallel foil to the cultivated "cowboy" image of Ronald Reagan. As Reagan moved from Hollywood into politics, first as the governor of California, then as the president, Wegner argued, he held onto the image of a do-good, heroic cowboy, an image he developed and honed as a movie star. And, Wegner argues, as the legend of Reagan-as-cowboy grew, the legend of Brown-as-terrorist also grew, and as another classic western, The Man Who Shot Liberty Valance, taught us, "When the legend becomes fact, print the legend."

Now, whether you buy Wegner's take on the issue or not, Santa Fe Trail did damage John Brown's historical "image" in other ways. Specifically, in its portrayal of Brown as a sort of "Great White Hope" for the slaves for whom he fought, it damaged his reputation among black communities in the US. Up until that point, Brown was recognized as a solid champion of emancipation and civil rights, but not as the white hero black folks needed. Indeed, WEB DuBois wrote a nuanced biography of John Brown in 1909 which suggested that Brown was frequently aided by radical black abolitionists, both free and enslaved, both in his Kansas battles and in his raid on Harper's Ferry. So, it could also be suggested that following Santa Fe Trail, the community that had previously recognized and championed Brown's violent efforts to hasten emancipation -- i.e. the black community -- found new reason to pillory a former proponent of civil rights.

Now, while I find Wegner's theories interesting, at the end of the day I think /u/lojafan's answer probably holds more water: there is way too much US history to cover in far too little time, and it's a lot easier to champion (from a curricular perspective) an apparent "faultless" hero such as Abraham Lincoln or Martin Luther King, Jr., than it is to champion a flawed and violent hero such as John Brown or Malcolm X.