From my limited knowledge this mostly comes from colombine and how the kids where using DOOM as a platform for this negative behavior (someone correct me if i am wrong)

It takes one or two cases of people being idiots to ruin it from everyone else.

Interesting note too on the 'shooting zombies' thing, One point in the banning report was that they where 'Humans, infected with a rabies like virus' not technically zombies... cause people know the difference