Several airlines offer flights between the main cities of the Philippines, and there is also a train service on the main island of Luzon. Getting between the islands is best done by ferry, although these services are sometimes overcrowded, and there are practically annual tragedies involving the vessels, so you might want to just use the more modern safer looking ones.
You can hire cars in the cities, and tour the fascinating rural areas at you own pace, or even find an untouched beach to relax on.