Because the other nations once controlled by the Ottomans gained independence under Christian nationalist regimes. Bruce McGowan, citing Bulgarian historian Nikolai Todorov, notes that by the 1830s the population of the Ottoman Balkans was 33-42% Muslim.^1 While this estimate includes Bosnia and Albania, it's clear from the sheer numbers that there were plenty of Muslims outside of those regions too. In particular some parts of southern Bulgaria, as well as Macedonia and the Dobruja region also contained majority Muslim populations, and Muslims made up significant minorities in many other parts of the Balkans.

So what happened to them? The answer is that as the Ottoman Empire lost control of territory, the Muslim population either fled or was ethnically cleansed. The first major instance of this was in the late seventeenth century. Cities like Buda and Pecs had been largely Muslim, but their populations were either massacred or fled following the advance of the Habsburgs into Hungary. The Muslims of Serbia largely fled once that country gained autonomy in 1830, moving instead to Kosovo and Macedonia. Many of the Muslims of Bulgaria likewise fled once independence was achieved, as between 1880 and 1945 574,000 of them left the country,^2 a number roughly equal to the current Muslim population of Bulgaria, which still represents about 8% of the population today. Hundreds of thousands more were forced to assimilate or flee during the 1980s as the state adopted repressive measures against them. The Muslims of Greece were forcibly transferred to Turkey by mutual agreement between the two countries in 1923, uprooting some 500,000 people. Bosnia as well has a much lower percentage of Muslims today than it did in the past, a result of flight, persecution, and genocide.

However, Bosnia was integrated into the Habsburg Monarchy and then into Yugoslavia, two states which had to place a great deal of emphasis on balancing the interests of their various ethnic and religious groups and could not afford to openly persecute the Muslim minority through religious nationalism. Albania likewise had a highly heterogeneous population and after independence its nationalism was not based on religion. But in Bulgaria, Serbia, and Greece, the national identity was deeply connected to the Orthodox Church. There Muslim minorities were generally seen as foreign "Turks" no matter what language they spoke or what ethnicity they were.

1. Bruce McGowan, Economic Life in Ottoman Europe: Taxation, Trade, and the Struggle for Land, 1600-1800, (Cambridge: Cambridge University Press, 1981) 85.
2. Antonina Zhelyazkova, "Islamization in the Balkans as a Historiographical Problem: The Southeast-European Perspective," in Fikret Adanir and Suraiya Faroqhi, eds. The Ottomans and the Balkans: A Discussion of Historiography, (Brill, 2002), pp. 235-6.

I've written about the Albanian independence movement before, and noted that religion in Albania (meaning amongst ethnic Albanians) was not a major feature, nor seriously considered (many adopted both Christianity and Islam, using each to whatever extent was convenient). Several scholars have noted that for the Albanians, the benefits of converting to Islam while subservient to the Ottoman Empire were more to do with keeping up their traditional way of life: among other things it meant less repression, and the ability to keep arms, which was a major point for the rural, tribalistic Albanians.

While I can't expand this point to the Bosnians, I will note that in contrast to Albania, both the Greeks and Serbs had religion play a major factor in their ethnic identity (or at least more than the Albanians ever did), and used it to differentiate themselves from the Turks. Thus they had motivation to maintain their ties to Christianity, whereas the Albanians were far more fluid in that regard, and saw religion more as a means to preserve their ethnic identity, and not a major component of it.