The problem is there are plenty of uniformed infidels out there. The Qur'an is just one part of the Muslim faith that generally everyone focuses on. They fail to look into the Hadith - the traditions of Muhammad come in. It has volumes and volumes of stories where Muhammad how and it what situations versus in the Qur'an came to him. The Qur'an is often times incomprehensible the ahadith.

The focus of MANY ahadith is war -

In one hadith Muhammad gives 3 choices on how to deal with infidels - invite them to accept Islam, if the accept stop waring against them. If the refuse Islam demand them the Jizya (infidels tax) and if they agree to pay then accept it and don't harm them and finally if the refuse either of those two then seek Allah's help and kill them.

It is what they did then and what Osama bin Laden demanded in a letter to the American people in 2002.