Okay. First thing - this is not a done deal. The news is that Warner Bros. was approaching Affleck. There is nothing to say that he has said yes or is even considering his options yet.
And ignoring the above article, which cites interviews where Affleck said that "the years of superhero are behind me", that he had turned down a chance to be considered for directing Man Of Steel and because he was only interested in directing movies where he could also act ("I have to be part of a story I want to tell."), there are plenty of reasons why Ben Affleck directing a Justice League movie would not be the worst of all possible options.
In order of reasonableness, from least to most, let me address some of the complaints I saw on Twitter immediately following this story breaking...
"Affleck? Ewww... does no one remember how bad Daredevil sucked?"
Yes. Thankfully, Affleck had nothing to do with the writing or direction of that film. That was all down to Mark Steven Johnson, who also wrote and directed the first Ghost Rider movie. I'll be the first to say the Daredevil movie was flawed but blaming Affleck entirely for the failure of the Daredevil movie is like blaming the petty officers for the sinking of the Titanic.
Affleck is inexperienced as a film director.
So is Joss Whedon. While having a fair bit of experience directing television series and short features, up until Avengers he had only ever directed one full-length film. And all Browncoat-loving aside, Serenity was not a blockbuster success. And if you don't remember some Marvel fanboys freaking out over that when it was annouced Joss was directing ... well, you were probably a Runaways reader.
Affleck has no experience creating big-budget blockbuster movies.
By that logic, Michael Bay would be a good choice to direct a Justice League movie. And if you believe that, I've know a couple of Transformers fans who would like to talk to you.