I personally don't discount at all the notion that there was some cover-up of government incompetence surrounding 9/11 (I still can't get over Condoleeza Rice claiming that no one had anticipated an attack of this nature). But as for direct involvement in the attacks, I don't think there's any evidence of that.
I meant conspiracies about missiles or our own F-16s shooting down the plane in Pennsylvania, or some of the other assorted "way out there" imaginations described in the report.
As for government incompetence? I suppose there could be a coverup of that. Business as usual for politicians.