If you look at the most recent State Department reports on Turkey and Indonesia, you will certainly see numerous and agregious human rights violations but the reports also cite how these moderate (yes, moderate) civilian elected governments are trying to reform.
Quote:
Turkey:
Turkey, with a population of approximately 69.6 million, is a constitutional republic with a multiparty parliamentary system and a president with limited powers elected by the single‑chamber parliament, the Turkish Grand National Assembly. In the 2002 parliamentary elections, considered generally free and fair, the Justice and Development Party (AKP) won the majority of seats and formed a one‑party government. The civilian authorities generally maintained effective control of the security forces.
The government generally respected the human rights of its citizens; although there were improvements in a number of areas, serious problems remained.
Indonesia:
Indonesia is a multiparty, democratic, presidential republic with a population of approximately 241 million. In October 2004 Susilo Bambang Yudhoyono became the country's first directly elected president as a result of elections that international and domestic observers judged to be free and fair. Voters also chose two national legislative bodies in 2004: the house of representatives (DPR) and the newly created house of regional representatives (DPD). While civilian authorities generally maintained effective control of the security forces, in some instances elements of the security forces acted independently of civilian authority.
There were improvements in the human rights situation during the year and, although significant problems remained particularly in areas of separatist conflict, the end of the country's long‑running internal conflict in Aceh Province was a major step forward. The government faced an intermittent, low intensity guerrilla conflict in Papua and West Irian Jaya provinces; inter‑communal violence in Maluku and Central Sulawesi provinces; and terrorist bombings in various locations. Inadequate resources, poor leadership, and limited accountability contributed to serious violations by security forces. Widespread corruption further degraded an already weak regard for rule of law and contributed to impunity. Poverty, high unemployment, and a weak education system rendered all citizens, particularly children and women, vulnerable to human rights abuses. During the year the government devoted considerable resources and attention to the recovery effort following the devastating December 2004 earthquake and tsunami that left more than 130 thousand persons dead and missing in Aceh and North Sumatra provinces. The country struggled to come to terms with human rights abuses committed by prior governments.
During the year there were significant improvements in the human rights situation. For the first time, citizens directly elected leaders in 149 local elections at the city, regency (county equivalent), and provincial level. On August 15, the government signed a peace agreement with the Free Aceh Movement (GAM), which both sides implemented thereby greatly reducing human rights abuses in that province. In Papua and West Irian Jaya provinces, the government inaugurated the Papuan People's Assembly and took other steps toward fulfilling the 2001 Special Autonomy Law on Papua. Security forces showed increasing restraint in response to nonviolent separatist demonstrations in Papua. The government began an anticorruption campaign that achieved some results, including high profile convictions.
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We wont see western style democracies anytime soon, but it seems to me we should work with these moderate muslim governments and encourage and support further reform, rather than alienate them and their citizens and potentially create situations than feed the more radical elements.