The Yugoslav Wars were largely founded on ethnic divides which had existed long before the fall of Byzantium, and which both the Byzantine and Ottoman Empires had failed to remove - the fact that by-and-large the two dominant sides of the conflict were also divided on religious lines is primarily coincidental. This misconception is made more obvious when you consider that the first large-scale war crimes and ethnic cleansing during the Wars took place in the Croatian War of Independence, a conflict where both the Serbs and Croats - although different ethnic groups - were both demographically Christian.
To return to Turkey, both the Thracian and Anatolian components of the country are the most ethnically and culturally diverse areas of the Muslim world - although close to 99% of the population are demographically Muslim if one counts those who are not active practitioners of the religion, the long history of cultural interchange in this area of the world first under Byzantium and then under the Ottoman Empire makes the country as a whole quite tolerant in its outlook.
As such, it is a great shame that the atmosphere created by the exceptions to this rule has put you so thoroughly off returning.
