We got back from our trip this morning. We visited Manila, Puerto Galera, Cebu/Mactan Island, Oslob and Moalboal. Not one second did I not feel safe, we walked to dinner In Manila from our hotel, we walked around Green Hills and another area I don't remember the name, walked all over PG and Moalboal. Everybody was nothing but super friendly and helpful. We dove PG and Verde Island (got sucked to 110' by a sudden downdraft, not too funny), Cabilao Island (off Bohol), Mactan Island and Moalboal. We had such a great time, already planning to go back.....
There were Security Guards present, but they also acted as greeters, held the door open for me and were generally very friendly.
When Martial Law was declared in Mindanao, it was business as usual in the other parts of the country. Nobody seem to pay it any mind.
I am sure that, like in any other country, there are areas that one should avoid. Just like in Miami, LA, New York, Frankfurt etc. Use common sense and you should be just fine.