Atatürk appointed the military as the guardians of secularism back in the early 1900s. He felt it was especially important to have an iron fist keep state secularism considering Turkey's past as the Islam-based Ottoman Empire and the seat of the caliphate.

Thus any time there was an inkling of Islam in the government, the military stepped in to eradicate it. The most obvious example in my opinion is when Adnan Menderes was elected president in 1950 on a platform that was almost exclusively the return of the call to prayer in Arabic (it had been illegal to perform this act of worship in Arabic for decades, due to secularism and Turkish nationalism). He was pretty quickly overthrown via military coup, imprisoned, and executed after a sham trial. All because he was a threat to the militant secularism Atatürk instituted.