The moviemaker is preparing to start production on a follow-up to the 2013 blockbuster, Batman vs. Superman, which pits the two superheroes against each other for the first time on the big screen.
However, the casting choices have proved unpopular with some sections of the public, with films fans railing against Snyder's decision to cast Ben Affleck as Batman and Eisenberg as Superman's nemesis Lex Luthor, and hundreds signing petitions in protest.
Snyder has now defended his decisions, insisting fans of the franchise will understand once they see the film.
He tells the Los Angeles Times, "We know the material. Unfortunately, the fans don't know the material. So, we're casting according to what's happening in the script... I understand the canon. I'm not crazy. I know what these characters need from a mythological standpoint."
He adds of the backlash against Eisenberg's casting: "I think Jesse is going to be an amazing Lex. Let's not forget he was nominated for an Academy Award (for The Social Network). It's not like I just grabbed my friend to play the guy! This guy's the real deal."
Snyder goes on to brand the gripes "frustrating" but insists he does not pay too much attention, adding, "Some people are hating to hate... Just stop it!"
The highly-anticipated blockbuster, which features Henry Cavill reprising his role as Superman, is set to hit cinemas in 2016.