On the account of Uthman’s actions, many Muslims were not happy with him. The negative reaction of prominent Muslims is well documented, and a careful review of this, may perhaps give some insight as to why Uthman was eventually assassinated.
Talha b. Abdullah said to Uthman, “You brought new innovations into the religion that people were unaware of before and did not know about in religion.”
Al-Zubayr b. al-Awam one day said about Uthman, “Kill him, he has changed your religion.” The people reminded him that his own son stood at the door of Uthman and protected him. Al-Zubayr replied, “I would not dislike that Uthman be killed even if they start by killing my son.”
Abdullah b. Masud used to say about Uthman, “The best of truth is the Book of Allah, and the best guidance is the guidance of Muhammad, and the most evil things are the ones which have been innovated, and every new thing that has been brought up is bidah, and every bidah is deviation, and every deviant is in the Fire.”
Amaar b. Yasir, at the Battle of Siffeen, said that when the people were asked why they killed Uthman, they answered, “We killed him because of his ihdath (new innovations).”
Sa’d b. Abi al-Waqqas was asked about the motivations behind Uthman’s assassination and he said, “He changed – and he has been changed. He did good things and he did bad things. If we do good, then we have done good, and if we do bad then we ask forgiveness from Allah.”
Malik al-Ashtar describes Uthman in his letter to him as “the one who throws the injunctions of the Qur’an behind his back (al-nabidh li hukm al-Qur’an),” and “the one who has turned away from the tradition of the Prophet (al-haid an sunnat al-Nabi).”
Lady Aishah, the wife of the Prophet said to Uthman, “How quickly you have deserted the tradition of your Prophet. His hair and his sandals have not yet decomposed” [the sunnah fell apart quicker than the remnants of the Holy Prophet]. She also said to him, “You have abandoned the tradition (sunnah) of the Messenger of Allah.”
Muhammad b. Abu Bakr, the son of the first caliph Abu Bakr, said to Uthman, “What religion do you follow?” Uthman replied, “I follow the religion of Islam,” after which Muhammad told him, “You have changed the injunctions of the Book of Allah,” and left angrily.
Abu Dharr al-Ghifari, a close companion of the Prophet, said to Uthman, “By God, I have seen affairs and events that I cannot even recognize” [that they are neither in the Book of Allah, nor in the traditions of the Prophet]. He also said, “I can see truth which has been extinguished and falsehood (batil) which is being resurrected and an honest person whom people are doing wrong to and are saying that he is a liar.”
Such comments indicate that many prominent companions were displeased with Uthman’s policies and his implementation of the Qur’an and the sunnah. The accusations they levied upon him, bidah and ihdath – both meaning innovation – are very serious in Islam. After he was killed, his body was left for three days – unwashed and unburied. Finally, Marwan b. al-Hakam and three of his disciples recited the funeral prayers over him, but the people of Madinah, who had refused to participate in the funeral prayer stoned them. They did not allow his body to be buried in the same cemetery (as the Muslims), thus he was buried outside the boundaries of the al-Baqi cemetery. Later on, when Mu’awiyah b. Abu Sufyan took power, he extended al-Baqi to include the grave of Uthman.
 Ansab al-Ashraf, 5:29
 Sharh Nahjul-Balaghah, 9:36
 Hayliyat al-Awliya, Sharh Nahjul-Balaghah, 1:38; 3:42; Ansab al-Ashraf, 5:36
 Kitab Siffeen, 3:19
 Al-Imamah wal-Siyasah, 1:48
 Al-Futuh, 1:40; Ansab al-Ashraf, 5:46
 Ansab al-Ashraf, 5:48; Al-Futuh, 1:64; Sharh Nahjul-Balaghah, 3:49
 Al-Tabaqat, 3:73; Al-Bidayah wal-Nihayah, 7:193; Al-Kamil, 3:178; Al-Imamah wal-Siyasah, 1:44
 Ansab al-Ashraf, 5:53; Sharh Nahjul-Balaghah, 3:55
 Ansab al-Ashraf, 5:83; al-Muntazam, 5:58
When Power and Piety Collide by Sayed Moustafa al-Qazwini