There is a lot of stuff that attempts to cast doubts, for certain. And my apologies for my memory not being able to instantly recall all the events that were the inputs to the conclusion. I remember things that are important to me, these details simply aren't.
All that is needed is to read the words of bin Laden himself, and the "call to all Muslim's to attack the U.S. & its citizens". I don't know how it could be made any clearer or undeniable than that. There are videos, statements, and interviews that all have this information. In addition, his endorsement of Ramzi Yousuf for the 1993 attacks on the WTC are clear - which shows motive, intent, and means. In the words of bin Laden himself, he has "declared war" on the US.
In addition, in a video by shown by Al Jeera in Oct 2004, bin Laden essentially admits to being responsible and even names a few of the "19" and blesses them all.
An indictment of all Muslims and the Muslim religion? Not by any stretch.
Reason beyond any doubt that US citizens have justifiable grounds for believing that bin Laden and Muslim terrorist were part of the attacks on the WTC? And is this not enough justification to hold some level of apprehension and distrust towards Muslims from the middle east and their motives for wanting to enter the US? It appears that folks in the US are the only ones that think so.