One, I guess, must come to accept such a thing as a sign of the times... The Age of Imperialism is remembered for it's atrocities to those "unlucky" enough not to be born white Europeans (though that sometimes was not enough). It can be found in much of the fiction and science fiction of the period, and even into Professor Challenger's speech, as he refers to the natives of Brazil as savages and naturally less well mentally endowed as the British (especially him). But even the simple acceptance of this fact of life does not clear up certain points of contention.
For example, Lord John Roxton being "the Flail of the Lord." In the early chapters of The Lost World, Roxton relates his personal war against the slave drivers of South America. Stating matter-of-factly that there comes a time where a man has to stand up for what's right, he became known as a great hero and liberator of slaves up and down the Amazon. Yet, at a later point, he leads the charge in the assault upon the ape-men, expressing a thorough disgust and a blood-thirsty desire to rid the world and his family tree of them. Confusing? Yes. The only reasonable justification of this is the Imperialist mentality that the people of other nations required the Europeans to settle their problems. Therein, the Flail of the Lord wasn't fighting the slave drivers because he was being noble... He was doing it because he was a Great White Hero and it was his duty to save the "savages." This then sets up Roxton as being as perfectly racist as anybody else at that time.
But the greatest confusion lay in Conan Doyle himself. Conan Doyle was of Irish decent, and in Victorian literature and society, the Irish was used as a caricature of everything primitive and savage. This betrays itself in The Lost World in that Malone is Irish and must face that same bigotry Conan Doyle himself must have faced. Why he would do such a thing to himself, considering that he was a strong proponent of tearing down that stereotype, is anybody's guess. Why he would compound racism in his book while being the victim of it himself is also anybody's guess. However, he does get his redeeming stab at satire in when we see that, for example, Prof. Challenger and the chief of the ape-tribe appear almost identical as the stand beside oneanother, save the red hair of the latter.
So, what does one make of all this? In all it's confusion, it would seem to be one of those things one must accept as a fact of life. The Lost World was written in racist times, and reflects that amply. It is the kind of thing that one simply has to ignore and hope that it will not affect thier enjoyment of the adventure.