First went there when I married in 1986. On the return journey from our honeymoon our locked luggage was put at the back of the bus behind the back seats. During the journey, someone with a knife cut through the luggage and took money and passports. Ironically we put these items in the luggage because we were worried about bag snatchers pinching the small bags we were carrying. All sorts of problems, with the police wanting a little sweetener to provide us with the necessary crime report, to take to the embassy for a replacement passport to be processed.
Been there 10 times since and walked many miles around Manila, Cebu and Danao, but never encountered any problems. Although I was wary about walking in some of the sketchy areas.