Should note that the villains picked would cry and freak out.
Kingpin is a true blue 100% New Yorker and would freak out that terrorists killed so many people. Especially since he rules the underworld from a similar high rise building and would stand to lose huge amounts of money.
Juggernaut was in the process of becoming a moral fag plus he knocked down ONE of the WTC buildings already.
Magneto is obvious in that he is a moral fag
As for Doom? Besides the notion of Doom being pissy because the WTC attacks were cowardly as shit there is another more plausible reason:
Doom cried for PR purposes.
He knew if he didn't show some level of dismay, America would put his name on the list of dictators they wanted to overthrow post-911. So a couple of crocodile tears for the cameras as Doom mentally curses the media for making him do so