Because Nolan's fanboys see him as a genius who can do no wrong and they have to square that circle somehow.
Nolan is a genius, and he has done no wrong.
Memento
Insomnia (supposedly, I have not yet watched that one, the DVD is next to my TV)
Batman Begins
The Prestige
The Dark Knight
Inception
The Dark Knight Rises
There's no "squaring a circle". I've seen six Nolan movies, and each of them is excellent. The three Batman movies are the three best comic book movies of the past 15 years in my opinion and several other people's. Best character arcs, best action sequences, the best villains, best soundtracks, only oscar nominations, RT scores of 85%, 94%, and 88%. If you look at the most respected comic book movies, Nolan is the only director to have had genuine success making other kinds of movies.
Nolan's batting 1.000. Is Goyer batting 1.000? No. Goyer's record is tarnished by several misfires.
But hey, if you don't like the intensity of Nolan's films, you should go watch the idiotic
Thor 2. It's playing in theatres now, it's a different style, they have a crazy scientist character streaking outside Stonehenge for comic relief, oh my that is so much more fun

.
Either that, or you can think about why Goyer is assigned blame for some of the problems. It could be that he wrote the dialogue for Batman Begins, which is considered the weakest one. It could be that he is the one who fought for the inclusion of Talia Al Ghul, where TDKR would have been a little better without Talia according to many. It could be that he was least involved with TDK, which is considered the best one. Think about it.