You need to brush up on your history of Turkey - everything that happened in the past century. The ruling class even in the Osman Empire was never all that religious - most ruling classes aren't, I find, as being truly devout would limit their ability to be self-serving as well as possibly harming their diplomatic interests - but the Osman Empire came to an end, and the Republic of Turkey is a rather different entity. Mustafa Kemal was a thoroughly Westernized army officer, and built a state that is probably even more aggressively secular than France. Him being born a Muslim and remaining a Muslim in name doesn't change any of that. There is a relatively small but immensely powerful class of secularists in Turkey, who look down on devout Muslims and want to keep them down. Mustafa Kemal was one of those, and many of the governments since. Obviously the government now is formed by a party representing in the first place the devout Muslims (though it also has most of the even smaller group of Turkish liberals, fyi), but the secularists still control the judiciary and the army. So no, the generals aren't Copts - there aren't any Copts in the Asian part of the Middle East to my knowledge anyhow, the Christians in Lebanon, Palestine, Iraq are Assyrians and Maronites, while the ones in Turkey are mostly Greek Orthodox - but they don't make it to the powerful army positions unless they are aggressively secular and nationalistic. The last coup they did actually execute was against a party that was too Muslim for its taste; the AKP has originated in that same party but is a fair bit more moderate now - the threat of the AKP lies more in its remarkable success and popularity.

While we're on the topic, I think a lot of Americans who blindly choose the side of the secularists over that of the "Muslim-Democrats" of the AKP might reconsider if they had a clue about what said secularists really thought. Maybe those Americans just think that anyone opposed to Muslims must obviously be in favour of America and the West. Well, think again. The CHP, the secularist party, is consistently more hostile towards the US - and certainly towards the EU - than the AKP is. A part of that may just be because they're in the opposition and the AKP is in government, but when you see some of party leader Baykal's statements, you'll see that there's much more to it than that. Between those two parties - the other two major parties in Turkey are an even more nationalistic party, MHP, and the successor party of the pro-Kurdish DTP, which is mostly moderate except for the inevitable ties to the PKK, but is unlikely to make it into the government any time soon - the AKP is most definitely the saner and more pro-Western one, and the one I would vote for myself, as I think would most Westerners if they had time to study the party positions (okay, some of them might vote DTP as well). And still between the two of them (the DTP has acknowledged the genocide and apologized for the Kurds' significant role in it), the AKP is the more likely to admit to the genocide, because the AKP isn't as nationalistic. Whether or not religion was a more important factor than politics and nationalism at the time the genocide actually happened, it's clear that religion is not a major factor in the refusal now to acknowledge it.

And then as for your blaming the two world wars on religion, that makes little sense to me... certainly, the Balkan Wars had a link to religion, though I wouldn't call it the dominant factor, but the Balkan Wars are only a small part of the factors leading to WW1 (I'm assuming your reasoning to claim WW2 as well is merely that WW1 led to WW2). One would think that you'd not blame religion for even more of the world's ills than its detractors already do, considering how religious you are yourself.