It seems to me that one of the overriding themes to the poem is the movement from childhood to adulthood. The poem stresses the idea of presenting a series of test cases to assess whether this child has passed these benchmarks to move from child to adulthood. The opening line helps to establish this, in that while others are enduring a loss of focus and discipline, the adult is the individual who can "keep" their head. This opens a series of conditions where one can identify if they are acting as child or as an adult. Enhanced by the idea of self trust, avoiding deception and hatred, the first stanza helps to bring these ideas to the forefront. Such benchmarks are seen throughout the poem, as well, confirming the theme of passage from child to adult as critically important.
The theme of this poem is that the speaker wants his son to grow up to be what he thinks of as a man. To the speaker, being a man involves the sorts of virtues that upper class English people of Kipling's day believed in. These were the values that allowed England to conquer their empire, or so they thought.
To Kipling, these values include being able to maintain confidence in your own abilities because you know you are better than those around you. He also values being very bold -- being willing to risk everything. Finally, I would say he values being able to deal well with all sorts of people -- those above you and those below you.
If you can do all these things, you will be man.