Films are always always going to depart from books. The media are a lot different. They're probably targeted at different audiences. I don't remember many of the details of the Bourne books; it's literally been decades since I read them. But Ludlum's books were cut from the shadowy conspiracy/spy/etc. cloth whereas the Bourne movies are primarily big budget modern Hollywood action adventure. (Which I don't much care for and probably wouldn't have loved even if they kept characters and other relationships between the books and the films.)
Directors are also just going to have their own visions. In many cases, they're just not going to like some of the creative choices the original author made--and there are a lot of fingers in Hollywood development projects in any case.