There's no reason to be concerned about security and safety throughout most of Turkey. The Turks will tell you -- quite emphatically -- that they are not Arabs even though they are predominantly (97%) Moslem. It's fairly evident from their membership in NATO and their application for full membership in the European Union that their sympathies are much more Western than Arab. In fact, their tour guides almost gloat over the fact that they don't care that they don't have any oil because they have a resource that sells for three times the price of oil on the world market and that without it, in the desert, you die. This resource, BTW, is called "fresh water" -- and the Arab countries are very dependent upon it.
Turkey is a very large country. There has been a small amount of Kurdish unrest is a small region in the southeastern corner, which is hundreds of miles from any of the areas where cruise ships call. It does not pose any danger whatsoever to the areas where you are likely to go.
Additionally, security in Turkey is very tight, especially at places like airports, where terrorist groups are likely to strike, and at many of the tourist attractions where there's concern of both terrorist threats and heists of various treasures.
I would not hesitate to return to Turkey!