It is strange isn't it...
I had read that the cresent moon and star was adopted by the ottomans after they took constantinople...
Which had been using this symbol for many years before...
Another possibility regarding the origin of the flag dates it back to the ancient Greek and Roman periods. It is argued that the city of Byzantium was dedicated to the Greek goddess Artemis in 667 BC, whose symbol, the crescent, was used as the symbol of the city and its coins for around 1000 years between 667 BC and 330/381 AD. After the Roman emperor Constantine the Great, who endorsed Christianity, made Byzantium (now known as Nova Roma, which, after Constantine's death in 337, became Constantinople) the new capital of the Roman Empire in 330 AD, and Theodosius the Great made Christianity the official Roman state religion by a law in 381 AD, the Star of the Blessed Virgin Mary was added next to the original Crescent of Artemis. This star is also commonly found on the icons of the Greek Orthodox Church to this day. Following the conquest of Constantinople (today's Istanbul) by the Ottoman Sultan Mehmed II in 1453, the crescent-and-star of Constantinople was adopted as the symbol of the Ottoman Empire, which eventually spread to the other Islamic land with the Turkish conquest of these areas starting from 1516; and eventually became regarded as an Islamic symbol.
From wikipedia 'http://en.wikipedia.org/wiki/Turkish_flag'
But this could be a theory.. no one really knows