Travelling alone in the Philippines is relatively safe for both genders. Backpacking is something that happens a lot in the Philippines and the local people have grown accustomed to seeing both solo travellers and groups of friends backpacking through the country. Ease of transportation makes it easy to get around. Travelling solo in the Philippines is absolutely OK, but since the places you are going to will be filled with travellers, both foreign and locals, you probably won't be alone for long.
Filipinos may be surprised to see a solo female traveller by herself, but this is more of a concern due to their culture, rather than an actual danger that is there. Be confident in travelling solo as a female in the Philippines. Most of all enjoy your backpacking adventure in the Philippines.