I think the fundamental thing is Turkey no longer feels like it needs the West for protection. For centuries Turkey lost ground to Russia and its Balkan allies. Then the Soviet Union for a time looked even stronger than Russia. Now, the Sov's have been replaced with relatively weak successor states on Turkey's border. Bulgaria and Romania are no longer in a Warsaw Pact. So, NATO isn't as key as it was.
Plus, being a good NATO ally isn't translating into EU membership as Turkey hoped. France is adamantly opposed and is getting support for its opposition. The US has been supportive but has limited influence on the issue. So, they wonder, what has NATO done for me lately?
Third, Turkey's occupation of half of Cyprus has really created distance with Europe and has somewhat isolated it.
Fourth, the traditional secular parties lost a lot of credibility with how they were governing the country, leaving the military to step in once again. Then came the Islamists, who looked to the voters like viable reformers. Because of the history, the military has been very reluctant to step in again and remove them, although it is a possibility.
Initially, it appeared the Islamists were going to bring Turkey into the EU and firmly into Western style democracy. In other words, they would be market oriented reformers with only an Islamism light. Only relatively recently have they actively pursued ties with radical Islamic states and until recently had a fairly open alliance with Israel. As their popularity has waned they have played the Islamist, anti-Israel card hard to try to salvage themselves.
Finally, the invasion of Iraq was hard for the Turkish government because it was unpopular there for all the reasons it was unpopular in Europe and unpopular in the Muslim world. Turkey came close to allowing US access to transit but in the end said no, which strained relations with the Bush administration.
It seems to me the only way the Bush administration could have done a better job with Turkey is not to have invaded Iraq in the first place. I don't think it had anything to do with not playing the game well.
I was wondering about the impact of the invasion into Iraq and you answered that. Unfortunately, neo-conservatism works against its own best interests at times.
I think the failure to gain EU membership is a big disappointment also. Once again, France working against the best interests of the West.
The real cause, as I read it here, is the relentless march of islamism.