Sufism
Even proper, formal Sufi orders have suffered persecution for various reasons. In recent times the most notorious example was the  outright banning of Sufism in Iran. This happened in spite of the famous Amman Message, a joint declaration made by over 200 of the most noted moderate Islamic scholars in a conference in Amman, Jordan, in 2005, stressing that Sufism is very much 'part' of Islam.