Have been to numerous places in both the Philippines (Manila, Anilao, Coron, Malapascua, Cabilao, Donsol) and Indonesia (Komodo, Nusa Lembogan, Raja Ampat, Bunaken, Bali, Lembeh).
Never felt unsafe. Just use your common sense (as you should in every other coutry or city) and you will be fine.