Yeah, that Marvel 9/11 comic is some of the silliest, most emotionally-manipulative nonsense I've ever seen in my life.
I get what they were going for, and their hearts were in the right place, but as you pointed out in the Marvel Universe something like 9/11 happens every Wednesday, and some of those same characters standing there crying about the Towers are usually the perpetrators - and in many cases have done FAR worse. 9/11 would be small potatoes for a genocidal lunatic like Magneto, why would he even give a sh*t? Other than someone else doing it before he could? Same goes for Doom and the rest. Dumb. Were they just upset that the terrorists who hijacked the planes weren't Officially-Licensed Super-Villains or something? "How DARE they do Exactly What We Always Do, but without costumes or code names? There are RULES and PROCEDURES to flying planes into buildings!" What the f*ck?
People often gush about it being so awe-inspiring, but really, it was stupid. Well-intentioned, for sure. But objectively stupid. You literally have to ignore just about Every Marvel Comic Ever Printed for that issue to make any sense at all.