Brawn has not made any public comments but it seems clear that someone is not happy with the performance of the Mercedes F1 team. The team has done well in qualifying and has paid out big bucks for big name drivers but the results in relation to the investment just are not there. Somebody had to take the fall and Brawn is that somebody.
Mercedes apparently thinks a single director for modern F1 does not work due to how complex the sport has gotten. BenzBoost would argue not having a single person at the helm could lead to dysfunction and power struggles. Regardless, Brawn was not willing to stay on in a capacity other than the head of the team so he will step down.
What will happen next year to Brawn as well as Mercedes? That is anyone's guess but major turnover is taking place for the Mercedes Formula 1 effort.