I have a few general thoughts that hopefully will put you at ease:
1). In my experience there are few surprise protests in Turkey. They are generally known/announced in advance. Simply avoid areas with planned protests - good advice regardless of the country you're visiting. In big cities (Istanbul and Ankara) check with your hotel when you arrive to ask about areas you should avoid.
2). Tourist areas in Turkey are quite safe. You will spend most of your time in these areas. All of the areas you listed are well known/visited tourist locations.
3). Most non-tourist areas are safe. Even if you get lost and walk or drive way off course you will almost always be just fine. Your biggest risk will probably be aggressive merchants or people on the street selling things. That being said, every city in the world has a bad part of town that should probably be avoided.
4). If by some odd chance you do end up in an area with a protest walk away. The protests are targeted at the government, not tourists. Any risk to you would be inadvertant.
5). Check with the State Department for any travel warnings or advisories before you leave: http://travel.state.gov/content/passports/english/alertswarnings.html.
6). Avoid unsettled regions. I'd steer clear of any anything near the Syrian border - south of Antakya (or maybe even Iskenderun) and south of Gaziantep. There is also a longstanding advice to avoid the far southeastern corner of Turkey due to ongoing issues with the PKK. None of the destinations you listed are in these areas.
I encourage you to go. Turkey is dense with historical sites and cultural experiences. I think you'll have fun.