I would say that using the word "comment" is too weak to describe the theme of this novel. It is definitely a "condemnation" of colonialism. Conrad believed that greed was behind colonialism. Why else would one country use its might to subdue another? It has to be about the money - loot, ivory, gold - other things that have value on the world market. The colonizing nation often veils its greed with lofty phrases such as duty, responsibility, converting the masses, improving native life, but as we see in this novel, often what happens is exploitation and worse, cruelty and inhumanity to our fellow man.
Historically, the purpose of exploration was to find gold, or trade routes (which would result in more gold for a nation), or more national resources, or more living space. Sometimes nations explored for purposes of evangelizing nations. No matter what the original purpose, however, Conrad shows that if a nation shirks its duty towards cultures that are less developed than they, the results are destructive and, in this novel, evil, for those colonized countries. Why? Because, man's heart is dark!
"Heart of Darkness" certainly comments on the negative consequences of the Imperialistic exploitation of Africa; however, I'm not sure we can say that it clearly condemns it. Critics disagree to what degree Conrad suggests that the colonization of the Congo is flawed. Some believe that he does; other believe his entire novella is but another example of the kind of aloof, self-serving European attitudes that caused such exploitation in the first place.
The novella certainly is a comment on the evils of materialism and the destruction of humanity and good that can occur when human beings quest for such materials things at any costs--"the horror" that exists within each of us if our own greed is not kept in check.