The Burton/Schumacher Batman movies were a separate continuity/universe from the Christopher Nolan movies.
Nolan's movies were a "reboot" of the franchise and character.
In an old interview with Nolan, he explains the studio's mindset.
"When I was looking for what to do next, one of the things I heard about was that Warner Bros were looking to restart Batman. After the success of Spider-Man, they felt they ought to get their big guys off the bench. The great part was that they wanted to refresh and invigorate the franchise, but didn't have any specific concepts and were essentially looking for someone to come in and tell them what to do. It's pretty unusual to have this sort of movie up for grabs."
So what is his take on the material? With the polished ease of a man who has been through a thousand pitch meetings, Nolan explains his idea. "The origin story was the bit that had never been told. I wanted to try to do it in a more realistic fashion than anyone had ever tried to a superhero film before. I talked a lot about films I liked, particularly the 1978 Superman, which is the closest thing to what I proposed. Obviously, some of it is dated, but it's an epic film, with a certain realistic texture. I wanted to make the Batman epic you expected to have been made in 1979."
Christian Bale elaborates on this in a separate interview
Batman Begins isn't a sequel to the Keaton-Kilmer-Clooney films. And despite the title, it's not a prequel. It's a complete reboot of the series. "We want you to forget there has ever been a Batman before this one," explains Bale. "[It's] his early days, the beginnings of Bruce Wayne. So you do see him as a very young boy, and then you see him at age 22, and then you see him again at age 29 or 30. A very large part of the movie is taken up with that before you even see any ears at all."