The article itself is actually pretty thin on details, adding to my speculation. It focuses mostly on how Warner Brothers and DC don't think David Goyer was the right man for the job, although he is still handling the script. Christopher Nolan is on board as a producer and "overseer" of sorts.
Columbus is probably best known as the director of the first two....and the two worst....Harry Potter films. While his films are almost always criticized by guys like me, there's no denying that they make money. Columbus has directed eleven films that have broken the $100M mark.