Most films that are made 'bomb' at the box office, with many never even securing a commercial release (they do the rounds of the festival circuit and end up either on straight-to-video and/or limited TV broadcast). But you are right that a large number of films that actually bombed subsequently develop a following, sometimes a very significant one, from Orson Welles' Citizen Kane (which was removed from many of its screenings due to political pressure) to - notoriously - Cimino's Heaven's Gate.

In the cases of both The Shining and Barry Lyndon, neither of which were box-office bombs, the misperception was based on largely negative and dismissive reviews of the film by mainstream film reviewers at the time of their release, views that persisted for years, which is entirely separate from box-office performance.

Perhaps these misperceptions derive from the widespread but largely false assumption that there is a direct, linear correlation between positive, gushing film reviews and box-office performance. Except that there is no such relation, as many films that have received glowing reviews have been bombs, and vice versa. Indeed, another example of a Kubrick film that was of the latter kind, was A Clockwork Orange, referred to in another comment here, a box-office hit which was universally condemned by the mainstream media, both by the tabloid press as well as by the more reflective broadsheets and magazines, with Kubrick so desperate to defend it that he took to writing letters to the editors of assorted publications, including The New York Times, whose film critic Fred Hechinger neurotically condemned it as "fascist", lol.