Well, they are only given so much space in Shounen Jump every week. About 17 pages or so. Each anime episode of Naruto has been averaged to be about 1.7 manga chapters. An episode of anime takes about two months from start to finish, so they have to plan ahead considerably. If the anime catches up to the manga, they have no material. This is why filler was created.

However, One Piece now has a much better system. They release about 2 episodes a month, so they stay consistently behind the manga.