I flew on Turkish Airlines this past summer from Tel Aviv to the States and back, and there was no problem whatsoever. Spoke with others who also flew with them and everyone was fine with it. You are only in the airport in Istanbul for a short time and the airport is fine–just make sure you get from one gate to the other as fast as you can because there can be a very short time to make your connection and the lines for security are long.
The airplanes are modern, the stewards and stewardesses are very nice, hospitable, and helpful. The kosher food was good. The price of tickets on Turkish is quite competitive, and the best part–two pieces of baggage for free, a rarity nowadays.