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?