The kids in those charter schools have parents who are much more concerned about their education than most of the kids in regular public schools. It takes some effort to get their kids into those charter schools; parents who make that effort are also the parents far more likely to check their kids' homework, help them with said homework, make sure they do their projects and turn them in, etc. A lot of the parent(s) in public schools don't even KNOW if their kid is in school on any particular day, don't know it's report card time, have no idea if their kid is doing work in a class or walking the halls or robbing the corner store.
Charter schools cherry pick their students; the minute a student becomes either a behavioral problem or an academic failure, they are quietly kicked out the back door to public schools, who must take everyone. Thus, the charter schools seem to have a better graduation rate.