The way I understand it, some of the other swimmers felt it was unfair that Phelps got put on the relay team because he didn't swim the 100 meter freestyle during the Olympic trials (top swimmers in the event at the Trials make up the relay team).

Although Phelps has faster times in the 100 than most of the guys and all things considered, SHOULD be on the team if the criteria is putting together the best team, one can surmise he was put on the team because of media pressure and more publicity for US swimming.