That was the entire reason why they included it. That was Snyder's 'big hook' which apparently he thinks was much smarter than anyone else did.
That's one of my hangups about the movie. Snyder could have omitted every flashback or montage dealing with the death of Bruce's parents UNTIL the moment Kal-El mentions Martha's name. Snyder could have used the opening flashback sequence and modified it into a simple montage of:
1) Glimpse of killer
2) Glimpse of gun firing
3) Glimpse of Thomas reeling
4) Glimpse of gun firing a second time
5) Glimpse of Martha reeling
6) The length of time in would take Thomas to utter "Martha"
7) Glimpse of young Bruce's face
In other words, a montage of images,
seven/eight seconds max, racing through Batman's mind before screaming at Superman, "Why did you say that name?!?"
Maybe it's cruel to treat part of the audience as ignorant regarding their knowledge of Bruce's parents or Clark's parents (both sets!)--or heck, even Diana's, lol--but the names are a part of American (if not world) modern day mythology. There have been movies. There have been television shows. There have been decades and decades of comic books, newspaper articles, SNL skits, etc. The freaking internet has been around since Al Gore created it! If there are people out there who don't know these central characters by now it's their problem in my opinion. /rant off