First, claims the Chinuch, the act of removing the foreskin is done to perfect the body. The foreskin is unnecessary, and the first religious act of a Jew is to perfect his body by removing this superfluous skin. The reason that Hashem did not simply create man without the foreskin was to show that though humans can attain perfection in this world, each individual must actively pursue his own path. One problem with the Chinuch's first answer is that in most cases, the brit milah is actually performed by the parents, not by the child. Perhaps a parallel can be drawn to education.
Parents are responsible to ensure that their child is adequately educated.
However, if they neglect their responsibility, the charge falls to the child, who must seek to educate himself as when matures. Similarly, the parents should circumcise their son, but if they fail to do so, the child must take care of it himself when he is old enough. The second answer given by the Chinuch is that the purpose of the brit is to separate the Jews from the rest of the world, as The Chosen People. In this sense it refers to the one between the Jewish people and Hashem. The physical act of circumcision is what shows that a Jew wants to join the fold.