In Iraq and to a large extent Syria, the battle is more between Sunnites and Shi'ites - in both cases including more secularly oriented people as well as religious fanatics - than between secular and Islamist.
And as for Turkey, I can't agree with that at all. Not to say that Turkey doesn't have issues, as the anti-Erdogan demonstrations underlined, but I see absolutely no reason to expect anything like what is going on in Egypt now.
I did not argue about who the war was between in Syria and in Iraq. It was my fault that my sentence was unclear. It was only referring to Egypt. The argument is about why there is civil war/clashes/unrest. All three states were also run by authoritarian dictators for decades. And now without the authoritarian dictator to stifle dissent, we have civil war.
We could also discuss the demographic dividends fueling the unrest. Older societies are unlikely to engage in such activities. 1/3rd of Egypt is under 16. In Syria its a little over 1/3rd. Iraq is about 40 percent. Turkey more stable at only 25% under 16. These are young, restless societies. Without an authoritarian ruler (who tended to be secular) to hold them together and to quash dissent, you will see a reversal to tribal loyalties that will split the societies apart. The Wilsonian borders are a big problem. This is why I expect Turkey to be a problem at some point soon. Though Turkey, in some respects, is more like a European society in 1848. Not modern enough. Not backward enough. A revolution/more civil unrest is possible. And here too the unrest may be fueled by secularists versus Islamists.