From the early pages of the novel, Tom's racism provides a backdrop to the action. When Nick visits him for the first time after moving to Long Island, Tom says he believes the "Nordic" races, to whom he attributes the development of civilization, are in danger of being overrun by nonwhites.
This is important because Gatsby, originally named Gatz, may well have a Jewish or Semitic background, meaning he would not be Nordic. We learn early in the novel that Tom has a narrow idea of who qualifies as "Nordic" when he hesitates for a moment even before including Daisy, his own wife, in that group.
In this passage at the Plaza, Tom insinuates that Gatsby is not Nordic. At this point, he understands that Daisy and Gatsby have been having an affair. He says he won't "sit back and let Mr. Nobody from Nowhere [Gatsby] make love" to Daisy. Immediately after this, he makes his remark about racial intermarriage, which he thinks is a terrible idea. To Tom, breaking up Daisy and Gatsby is about more than saving his own marriage: it is saving society from racial destruction.
Nick and the novel both reject Tom's racism. This is clear because the person Nick, and the novel, most romanticize is Gatsby, the man Tom overflows with contempt for to the extent he can hardly stand to be near him. For Nick, however, Gatsby is the heroic, if flawed and tragic, emblem of the American Dream, a figure he admires in spite of himself. He says of Gatsby, "there was something gorgeous about him, some heightened sensitivity to the promises of life."
Nick, on the other hand, dislikes Tom intensely. He continually casts him as brutal, unintelligent, hypocritical, snobbish, entitled and racist, and early in the book dismisses him with one the classical disses in American literature: "one of those men who reach such an acute limited excellence at 21 that everything afterward savors of anti-climax." Nick continually portrays Tom as the quintessential buzzkill: to be around Tom is to be in misery. From the start, Nick describes his old college friend as having "arrogant eyes" and "effeminate swank ... a cruel body."
In the end, Nick is an unreliable narrator who lacks the self-awareness to understand that his "cardinal virtue" is not his "honesty." We can't know for certain whether or not he is too hard on Tom, but Tom's own actions tend to bear out Nick's subjective feelings that Tom is a repugnant human being.