The pills stifled the libido (sex drive), so actually they were a form of chemical castration! In a world of sameness, there was no place for opposites of anything, including the sexes and intense emotional feelings. Jonas's mother explained to him that adolescents and adults took them until they went to the House of the Old. At this point, pills were no longer necessary, nor were family ties either, for that matter!
Jonas later has a "memory" imparted to him of a Christmas scene and wonders why the Community ever did away with the feeling of belonging in a family - with children, parents and grandparents. With an gnawing emptiness in his heart, he asks his father if he loves him, to which he replies that he "enjoys" him very much. Jonas then feels the "loss" of something he has never really known.
It is interesting that the first intentional act of rebellion "against the system" Jonas ever committed was when he decided not to take the pills. In a way, this is a crisis moment in that after having made this choice, for Jonas there is no turning back.