During the campaigning period before he became president, he used a predominantly red/blue combo to indicate his party colors.
Meanwhile, his primary opposition, the Yellows used... well... yellow. A brief history on that: During Martial Law to oust President Ferdinand Marcos, the rallyists used yellow ribbons to show their staunch disapproval of the late Dictator's decrees. Having suceeded in ousting the Dictator, it was then decided that the Yellow Ribbon be a symbol of the successful EDSA Revolution. By extension, for the sake of elections and the Aquino Family, the color yellow also symbolized their role in liberating the citizens from the Dictator.
During the previous presidential elections, her son, Benigno Aquino III, also known as Noynoy Aquino, used the color yellow in his campaign. It also helped that Cory Aquino, who was then merely just a citizen by that time (the one seated prior was Pres. Gloria Macapagal Arroyo), had passed away during the presidential election period. This created a massive emotional hype wave that practically ensured Noynoy Aquino's victory.
Fast forward to the near end of the term of Noynoy Aquino's presidency, he had not done a lot of things, playing passive for the most part and allowing corruption to still occur, and people had started becoming disillusioned. Thus began the dislike for the color yellow, which the president (and related liberal party members, such as Mar Roxas) unabashedly abused in every event that involved them.
Pres. Noynoy Aquino's presidential candidate pick, Mar Roxas, ended up being eclipsed by the now-infamous color yellow during the campaigns, due to inherent hypocrisy on their part and Mar Roxas 'trying' to be part of the community by doing things that the urban poor never do. He was hastily decimated by his own marketing approach. The color yellow, which related to the Aquino's martyrdom to stop the Marcos regime had now turned into a symbol of incompetence.
All the while Duterte was gaining traction due to his portfolio, his gungho casual no high-class nonsense approach endearing to the masses, and what seemed to be a genuinely real desire to help uplift the people in the far south of the country. It also helped that there's an inherent regional 'racism' between Tagalog and Visayan peoples, and that most presidents had been from the Manila/Northern regions. There was thus some push to elect a Visayan president.
Of course, that's just the short of it for the presidential election history, and the color yellow. I haven't touched the subject about the Cojuanco (Aquino-related family) controlled Hacienda Luisita, which was promised to be given to its farmers many years before, among other issues that arose during Noynoy's presidency.