The peaceful protest movement in Syria wanted political and constitutional reform so that all Syrians are included and that the Syrian people have the final say in who governs and on the source (constitution) of their authority to govern. Salafists do not believe in a constitution that is derived from the will of the people. They believe in imposing a particular and specific interpretation of Islamic traditions from the top down. 

For militant Salafists, the imposition of sharia, as they see it not as seen by the majority of Muslim scholar, was the end goal. The presence of many religious, sectarian, and ethnic groups in Syria made that vision incompatible with a Syrian society that is too diverse to reduce to a single monolith. These diverse communities knew that their struggle is existential, since Salafists framed the conflict as one between “Sunni Muslims” (Salafists), on one side, and apostates (murtadd), Alawites (nusayris), Shias (rawafid), and crusaders (salabiyin) on the other side. Salafists’ actions in Syria reflect this framing of the conflict. They accused residents of towns that are predominantly
inhabited by these communities of supporting Assad and they forced them out or placed
them under siege. Members of the security forces were summarily executed. In most cases, these acts were videotaped and posted on social media
to frighten civilians and force them to submit to their rule. Recently, the
chief religious mufti of one of the largest armed groups in Syria admitted to committing war crimes by killing prisoners based on their religious affiliation

In an interview with a Lebanese paper, Abdallah al-Muhaysini,
a leader of Jaysh al-Islam, which is a cover for Jabhat Fath al-Sham (aka Jabhat
al-Nusra), Istaqim kama Umirt, and Ahrar al-Sham confirmed what has been
reported since the start of the war in Syria. He admitted that his fighters target civilians who are “rawafid” and that they killed captured “nusayris” immediately. Salafist groups usually use derogatory sectarian names for warring parties to frame their war in Syria as being aimed at purging that country from non-Salafists.
This admission would have serious legal implications for individuals and governments known to have supported these groups, including Qatar, Saudi Arabia, and Turkey. Al-Muhaysini has had elaborate connections to foreign intelligence services and he formed working relations with all Salafist fighting groups in Syria which he urged to unite in a single army. He threatened those who refuse the unification. The admissions to war crimes and his threats could lead to his assassination.
https://i1.wp.com/majalla.org/press/wp-content/uploads/2016/09/SaudiMuhaisini_threatensHama2.png?fit=320%2C133https://i1.wp.com/majalla.org/press/wp-content/uploads/2016/09/SaudiMuhaisini_threatensHama2.png?resize=150%2C133EditorsSelected ContentAll,Human Rights,International Law,Law and Society,Syria,War and PeaceThe peaceful protest movement in Syria wanted political and constitutional reform so that all Syrians are included and that the Syrian people have the final say in who governs and on the source (constitution) of their authority to govern. Salafists do not believe in a constitution that is derived...