Caveat: this is perhaps a tangent on terrorism and only covers your first point and not the other 5 points.
I don't think that my government is being completely transparent about 9/11. I think it was a misnomer on their part to call Osama
and al-Qaeda terrorists. The attacks on 9/11 and how they were perceieved and projected by the American government and media were partially respsonsible for America's perception of Islam being a terrosist religion.
I think our government, our Christian president. the and media installed more terror into their citizens with the color-coded terror alert system.
Osama's and al-Qaeda's actions were not to install terror. Their actions on America were ideology and symbolic. The WTC, White House, and the Pentagon are idealogogical symbols just as much as (if not more than) concrete, material institutions. Osama and al-Qaeda' intent was not instill terror, but to attack American on an idealogical and symbolic level. Many Americans, Christians, and others are not aware of this.
Like An-jel said, every religious group has their bad apples. You are right Islam, like Christianity is are relgions of peace, but religion does not always cultivate tolerance and understanding. Religion when taking to extreme and fighting wars in the name of 'god'/'allah' is absurd and beyond my comphrension.
It's usually just a few people in any organizition that give that organization a bad name.