Before 1924, perhaps even later than that, it's not historically relevant to talk of secularism. The Young Turks, first and foremost, were the strato-political elite of the Empire and saw themselves as the saviours of their homeland, which should be freed from foreign subvertion, by a weak and pretty much no-good Sultan and which should be modernised to keep up with, and be able to stand up to, the western powers to which it was dependent.
Keep in mind that the Young Turks at the time of the Coup of 1908 is not the same group of people as later; and that Young Turks does not mean 'Atatürk and his secular friends'. There was a split between the so-called Liberal Entente, which was for the continuance of the dependende of the Empire on powers like Britain and France; and there was the 'Committee of Union and Progress', whose motto and goal was pretty much 'Turkey for the Turks'. That meant political and economic independence for their country. That meant get rid of any British and French influence and that by extension meant, liquidation of the non-Turkish elites controlling the economy of the country. Among the elite of the late Ottoman Empire, The Muslim element was only prevalent in the army; state-level banking and finances was controlled by the French, the British and the Germans; the railways were controlled by the British and the Germans; in the private sector, banking industry and trade were largely in the hands of the Greeks, the Jews and the Armenians; the British had seized Egypt and Cyprus, the Tzar threatened Konstantinye and every once in a while marched his army to its gates and the French saw themselves as protector of the Christians in Syria and Lebanon.
This elite of the army saw the Empire losing effective control of Crete and not gaining much despiting winning the war against the Greeks in 1896; then Austria annexed Bosnia for good, Bulgaria declared independence and took control of Eastern Rumelia in 1908; immediately after, Crete unilaterally declared union with Greece. Then it saw the Italians seizing Libya and the Dodecanese in 1911 and immediately after that, the Balkan Wars happened. The loss of Rumelia was the death spell for the Liberal Entente. The Three Pashas came to power 'thanks' to that loss.
In their eyes, that proved that all foreigners were against their country and were conspiring against it. That led to extreme nationalism and the minorities of the Empire, the demographic groups which we now consider as minorities that is, weren't just religious, they were also ethnic. And as such, they had to be dealt with. Note that, for example, the Alevis were not considered a minority because they didn't have a national conscience.
Consequently, the demographic group that ended up not belonging to a Christian millets, were considered by the ascending elite as the people who had to be given their country back.
