The Young Turks themselves were secular but they riled up and exploited the Muslim fervor of the uneducated masses to help them carry out the mass killings. Today, nationalism in Turkey is increasingly becoming conflated with Islamism. So when it comes down to it, as a country that is 99.8 percent Muslim, it does not matter to the Chrisitian minorities whether secularism or Islamism holds sway. Either way they are in constant danger - which is why the Pope made it his business to address this issue when he visited Turkey last November.
Then you could probably say the nationalist Hitler riled up the Christian masses to help him carry out the mass killings of Jews. Hitler must have looked to Talat Pasha when formulating his Final Solution.
That there was some ingrained hatred is undeniable, but the Muslim authorities were happy to keep the Armenians as second-class citizens, and only murder them when they got out of place. It took the secular Young Turks to turn it into genocide in a nationalist fervor (they claimed the Armenians were pro-Russian subverts).