I had the impression that Uthman was unpopular because he appointed his family members to positions of power. But a section in the wikipedia article about him gives the impression that the opposition to him was not purely political and people had dissatisfaction which they had not had during previous administrations.
Noting an increase in anti-government tension around the Caliphate, Uthman's administration decided to determine its origins, extent, and aims. Some time around 654, Uthman called all twelve provincial governors to Medina to discuss the problem. During this Council of Governors, Uthman ordered that all resolutions of the council be adopted according to local circumstances. Later, in the Majlis al Shurah (council of ministers), it was suggested to Uthman that reliable agents be sent to various provinces to attempted to determine the source of the discontent. Uthman accordingly sent Muhammad ibn Maslamah to Kufa, Usama ibn Zayd to Basra, Ammar ibn Yasir to Egypt, and Abdullah ibn Umar to Syria. The agents sent to Kufa, Basra and Syria reported that all was well--the people were generally satisfied with the administration, although some individuals had minor personal grievances. Ammar ibn Yasir, the emissary to Egypt, however, did not return to Medina. Rebels there had been issuing propaganda in favour of making Ali caliph. Ammar ibn Yasir, who had been affiliated with Ali, abandoned Uthman for the Egyptian opposition. Abdullah ibn Saad, the governor of Egypt, reported about the opposition's activities instead. He wanted to take action against Ali's foster son, Muhammad ibn Abi Bakr, Muhammad bin Abi Hudhaifa, Uthman's adopted son, and Ammar ibn Yasir.
Uthman's attempts to appease the dissidents In 655, Uthman directed those with any grievance against the administration, as well as the governors and "Amils" throughout the caliphate, to assemble at Mecca for the Hajj, promising that all legitimate grievances would be redressed. Accordingly, large delegations from various cities came to present their grievances before the gathering.