Like most of Milton's work, this sonnet is an expression of his religious faith.
Milton was tormented by his blindness, and understandably so. Even in Paradise Lost he alludes to it, in a manner some critics have considered an inappropriate intrusion of a personal element into the otherwise lofty and austere character of his epic poem. Though the religious message in "On his Blindness" is sincere, it's hard to escape the impression that he is straining to convince himself that he can bear his affliction patiently. The opening lines clearly convey the agony he feels over being denied his sight. He seems to assert that his sorrow is due to his inability now to serve God, but there is an obvious, and honest, sense of resentment that emerges—an anger at God for having allowed this to happen to him. This in itself is a remarkable admission for a man as devout as Milton was. But he concludes by making the point that all God requires is that a person have faith. The phrase, "They also serve who only stand and wait" can serve, and has served, as a motto for anyone with a handicap. This is a theme Milton was ahead of his time in expressing: that all are equal before God regardless of their disabilities.