The answer, pure and simple, is that the U.S. Government was unwilling to admit that one of its presidents had made a mistake on purely racial grounds. Although this might have been more likely in earlier days, the fact that it happened in the twentieth century at a time when racial bias was rampant acted as a barrier to righting the wrong that had been done.
The black soldiers involved were obviously wrongfully accused; the evidence of that fact now seems overwhelming. However, President Theodore Roosevelt, likely fearful of losing the white Southern vote, had most of the soldiers dismissed not for participating in the violence; but for disavowing any knowledge of it, which he deemed a "conspiracy of silence."
The matter was in fact investigated by a number of historians who believed that a number of the soldiers wrongfully discharged had won the Congressional Medal of Honor. This proved not to be true, and was an embarrassment for the historical community. Later, in 1970, another historian, John D. Weaver published The Brownsville Raid in which he argued that the men were innocent. His book led to a new investigation by the army which exonerated the men accused. Even so, the racial climate up until the 1970's was such that any action on the Brownsville affair was not likely.