If Somalia is muslim, why was it a problem for the Islams to gain so much power in the south, by 2006?

The group gaining power - known as Al Shabaab - in the south are not ordinary Muslims. They are terrorists whose actions do not follow the religion, they terrorize Somali citizens. 99% of Somalis are Muslims. They're not fighting against Al Shabaab because they don't like Islam - actually Al Shabaab's actions have little to do with religion. Religious terrorist groups distort the meaning of the religion or misuse it to justify their sick actions. Somalis fight against Al Shabaab because they don't want to be terrorized.