I see in this mornings Seattle Times newspaper that the current government of Turkey has arrested 50 high ranking military officers who, it's charged, were about to overthrow the government. Stay tuned. I am taking a RS 13 day Turkey tour in May/June so things had better settle down by then as I will not cancel my trip unless RS makes me.
I think it's highly unlikely that your trip will be cancelled. First: it's still a long time till your trip and second: even with military junta in power you won't be in any danger. Actually you probably will be safer. First time I was in Istanbul 1981, military junta was in power, soldiers were almost at every intersection, friendly and helpful.
Turkey has had periodic political unrest since before WWII. However, even with a history of several military coups, the only region that ever seems to see open violence is the south east Kurdish region. You should be fine.
Hopefully they can get this "political uncertainty" sorted quickly, as that might have a bearing on their admission to the E.U.?