In the case of Syria, about 75% of the population is Sunni and another 15% Christian. In Iraq, Sunnis comprise about 40% of the population [the Kurds are Sunnis as well]. In both cases, whether Sunni or Shi'a, the real reason why both were secular has to do with oppressive dictators who would deal with any opposition, religious or otherwise.
Osama is a Sunni, any coincidence there or should we not commit "genocide" against those who praised airplanes slamming into buildings and killing civilians thousands of miles away?
Khomeini was a Shi'a. Militant Islamic fundamentalists are not confined to one sect of Islam, although Whabbism as practiced in Saudi Arabia, the home of UBL, is among the most radical and conservative forms of the religion.
The vast majority of mulsims are not radicals.