I tend to read the story as critical of the English presence in India. The English in the story view themselves as "civilizers," but it’s clear that they have little idea of what Indian culture or values might be, and their own "civilized" values seem limited to trading horseflesh and drinking (a lot). The story suggests that whatever curse befell Fleete, its power was beyond anything the English could understand.

It’s also true that the way in which Strickland and the narrator act to save Fleete—by capturing and brutalizing the Silver Man (apparently—Kipling coyly omits those details, saying they are not fit to print)—suggests that the British attitude towards the Indians is to class them as subhuman. Fleete’s descent into bestiality can be seen as another way of "going native," something that must be stopped at all costs. Kipling sees Fleete as a kind of harmless fool, but one who does not deserve the punishment given him.

Kipling's story expresses the nineteenth-century British conception of India as in many ways an alien, hostile place. It is not just India itself, but anywhere "east of Suez," in Kipling's famous formulation, where Westerners are depicted as stranded without even the protection of their own "Providence."

Kipling, however, in spite of his even more famous phrase about the "white man's burden," is also stating by implication in "The Mark of the Beast" that Europeans really have no business interfering in the cultures of Asia, and that it is obviously wrong to demean non-European religions. This is why Fleete, by defacing the image of a god, nearly destroys himself in bringing on the Silver Man's curse. Think of how Fleete himself describes the smudge of cigar ash he has placed on the idol as just such a "mark," and then receives a mark in turn on his own body which first looks like an insect bite, but then turns into a huge, frightening lesion.

As always much of Kipling's imagery is from Scripture. In Christian eschatology the mark of the Beast is that of the Antichrist. As in the Bible, in Kipling's story there are repeated references to leprosy. A superficial reading would conclude that Kipling—or at least the narrator of his tale—sees a "satanic" element in the cultures of the East. But what does it mean that Fleete is the one who begins this particular conflict by placing his own mark of the devil on the inoffense god Hanuman?

You probably cannot find this because it is not specifically stated in the story -- you are supposed to infer it from what happens in the story.

To me, what Kipling is trying to show is that the British presence in India is often arrogant and ignorant.  He shows this through the actions of Fleete.  Fleete is arrogant enough to desecrate the image of the god with no regard for what the Indians might think of his action.

We see the ignorance of the British the fact that none of them seem to understand, at first, what is going on.