One of the other factors in this, is the fact that the two most iconic characters in the DC universe not only have the comic book legacy to compete against, but they are also competing against the various television and movie screen incarnations of themselves.
If you think about it, in looking at the Marvel Universe, when you say Iron Man, you think Robert Downey Jr. Captain America- Chris Evans. Thor- Chris Hemsworth. Professor X- Patrick Stewart. Wolverine-Hugh Jackman.
Not only do you have just one person that the overwhelming majority remember as the actor/actress playing the role, but for the most part it is thought of fondly. Everybody identifies with that one version of the aforementioned heroes, and that continuity goes a long way in establishing the resounding success of the Marvel Universe.
Conversely, the two franchises in the Marvel Universe that are currently being derided are Spider Man and the Fantastic 4, which both have the distinction of having multiple actors playing the roles of the protagonists.
In the case of the DC Universe, the current actors have the unenviable task of going up against their own history.
When you say "Superman" you don't think Henry Cavill, or Brandon Routh, or the guy from the 50's who played him on TV. You think Christopher Reeve. The squeaky clean, gee whiz type of Superman that a lot of us grew up and loved in the comic books.
And when you say "Batman", it is not Val Kilmer or George Clooney, unless you want to cry yourself to sleep. And it is not yet Ben Affleck. It is always Adam West, Michael Keaton, and Christian Bale. And each one was very different.
So now you have your 4th Superman (5th if you count what could have been with Nicholas Cage), and your SIXTH Batman. And neither one of these two that are currently playing these characters are entrenched in our minds.
That is a problem. I can't blame Affleck and Cavill for this. Batman and Superman have always, and will always be, #1 and #2 in the hearts of comic book fans as far as all time superheroes, especially considering that they were literally the first and second to exist. So we have nearly a century of kids being brought up with these two. It happens.
Marvel has the advantage of not having series of movies prior to these, so it allowed them, and the audience to familiarize themselves with one version of their heroes