I've long since come to the opinion that Bob's hatred for Man of Steel (and to an extent his hatred for The Amazing Spider-Man film, discounting his disturbing love for the mediocre at best Sam Raimi) revolves largely around the fact that it didn't mesh with his vision of what a superhero movie should be.
A vision that is, to be honest, somewhat mired in the history of comics.
The Marvel series have been largely upbeat, colorful films, with vibrant palettes and "witty" dialogue.
Now, from the perspective of DC... they tried that. When they handed the reins of the Batman franchise over to Joel Schumacher, and the horrid disaster that ensued. Now, when they went for the gritty realism route, with the inherently depressing Nolan trilogy, they had fantastic success, managing to rescue a franchise that seemed somewhat doomed at that point.
Part of that is that Schumacher went totally over the top, echoing more of the Batman TV show than anything else, but it's important to note that despite Bob's rosy-tinted glasses view of the golden age of comics, there were extended periods of the run of Batman where it was vastly closer to the TV show than it was to the far darker Batman of today.
I mean really: That iconic giant penny in the Batcave? A souvenir of his battles with The Penny Plunderer. Who committed penny-based crimes. Seriously.
Marvel has had it easy in some ways. Yes, the films are all very evocative of the comic book origins of the material, but to be fair Marvel always specialized in more human characters than DC, which gave the film teams significantly more to work with.
I agree that Man of Steel wasn't in line with the classic image of Superman as some sort of sans peur et sans reproche avatar of all that is good in the world. But that didn't bother me nearly as much as it apparently bothered Bob; in part because I tend to view a more modern take of classic characters as a positive thing, within limits.
The sticking point for a lot of people who disliked the portrayal of Superman in Man of Steel was how he dealt with Zod. Bear in mind that the comics had him reaching the same basic solution for something like twenty years as canon before rewriting it for the umpteenth time.