It's a matter of the director having a specific vision of how his Batman stories will become. In the first two films, Christopher Nolan wanted to bring Batman back to his roots, explore how Bruce Wayne became Batman, and how Batman became the legend he is (in the 1989 Batman film, when Vicki Vale asks Bruce why bats, he replies "They're great survivors"; in Batman Forever, we get a VERY brief glimpse of bats on Bruce's mind. That's all the motivation we get). Batman Begins was very much an origin story, showing also the training Bruce took to become Batman. The Dark Knight Rises follows soon after that story, as the ending of Batman Begins sets up The Joker to enter the story.
The thing is, I tried looking up the reason, and I can't yet find any quotes online from Christopher Nolan (see this article here for an expanded story on this). The next film, The Dark Knight Rises, supposedly takes place 8 years after The Dark Knight. It also features Bane, a character who became notorious for eventually breaking Batman's back. It's entirely conceivable that Nolan will include Robin in this film as his protege who can help him fight Bane. Nobody outside the film set really knows. Me, I'm looking forward to finding out in 2012.