Well, that's what most Muslims claim, but...
The tribes of Lapulapu and Humabon were part of Sri Visayan Empire in the 14th century. After the Empire was defeated by the Maja Pahit Empire of ancient Sumatra and Borneo, the tribes became part of a group who fled and eventually settled in the islands of the Visayas Central Philippines. Another group of those Sri Vasayans, that included the tribes of Datu Puti and Datu Sumakwel, went out and settled in Panay Island.
Somewhere in 1380, a certain Karim al-Makdhum (spelled as Karimal Makdhum in Pilipino) arrives in the Sulu Archipelago and started preaching Islam. Then Shariff Kabungsuwan, a Malay leader from the Malacca Sultanate and Sayyid Abu-Bakr Abirin, a Malaccan-born Arab comes to Sulu, strengthening Islam and hops onfoot to Mindanao. He became a Sultan and Sultanate of Maguindanao was born. Later, Chinese Muslims and Minangkabau missionaries preach even more Islam in the south.
So that is why Islam is now predominant in Mindanao, but how about Luzon and Visayas?
Manila and Tondo was ruled by Rajah Salila and Lakan Dula. These kingdoms were invaded by the Sultanate of Brunei and later, Salila became a Muslim and changes his name to the Arabic name "Suleyman." Lakan Dula didn't became a Muslim.
The Visayan remained Hindu, Animist and Buddhist. Also, they hated the Muslims and resisted Islam. For the Ilocano people of the far-northern parts, Islam was never part of their history as was Buddhism and Animism. So, since Lapu-Lapu was from Cebu (Visayas), the chances for him being a Muslim is quite slim. There are also tell-tail signs that both Humabon and Lapu-Lapu are not Muslim:
1.) The Visayans were well noted for their widespread practice of tattooing as well as the common custom of penile piercings (tugbuk or sakra). Pigafetta, who recorded Magellan's encounter with the Cebuanos, explicitly described Rajah Humabon as tattooed.
2.) There are records the consumption of pork, dog meat, and palm wine (arak) by the Cebuanos.
Islam was a little bit late in conquering Luzon and the Visayas.
The Spanish have introduced Catholicism just a few decades later after the Brunei sultan started preached Allah in Manila.