You have to be careful not to get a skewed version of life in the Philippines. It is safe to go there if you watch your step. Probably you should steer clear of Basilan and Jolo, just in the same way you should steer clear of Compton or South Central when you visit Los Angeles.
I lived in the Philippines during the Cold War, right after the fall of the Marcos Regime. The world was a very dangerous place then. There were communist rebels, muslim separatists, and CIA, KGB, and Red Chinese agents causing trouble all over the Philippines. It was safe then still, as long as you knew not to go to contested areas, or high crime areas. Any newspaper or embassy handout would tell you and still will today.
If you go to the Philippines, or anywhere for that matter, pay attention to the travel advisories, and be sure to pay attention to your surroundings. The Philippines is a country of law and order. Murder is illegal, kidnapping is illegal and as a result they are relatively uncommon and punished severely. The majority of the country and the majority of what you as a tourist have a chance to encounter, is safe. It is an unjust demonstration of "first world" arrogance to take those headlines and judge the entire country on them.
