I'm not surprised at all. Fight Club and the Matrix are movies that can kick the shit out of you the first time you see them.
Also, I think if you paid attention to the tastes of filmmakers, more often than not you'll notice that their tastes in movies are a lot more tolerant and less snobbish than that of the average movie-goer.
Especially from someone like Tarantino who speaks from pure enjoyment more than anything else.
But anyway, to be more topical. It sounds like they misquoted him, which is quite common in publications. I think he meant that it didn't affect or shock him because it was an image he'd already seen. And I think the comment on the matrix shooting in australia was really meant to be more of a funny idea than an actual diss or something.