That was a dark time in American history. Essentially the people of the PI felt that they were double crossed by the Americans. After being freed from the Spanish as a colonial power, they had the idea that they ought be left in peace and to their own devices. Instead American foreign policy took a turns towards imperialism and instead they were told "Silly brown people, you're our colony now."
This was the war that spawned the phrase "Civilize them with a Krag".
Press reaction in the states was mixed. Some papers considered the PI's inhabitants to be savages and encouraged men to volunteer on grounds of fighting what amounted to a race war. What were mainstream papers of the time made reference to Filipinos with openly racial slurs.
Some criticized the idea of America having an empire, then and now. Among them were populists and yes, Mark Twain.
That what now would be regarded as war crimes took place was well documented at the time and fairly well known. Water boarding, concentration camps, the burning of crops - no secret was made of it. Opinion in the US was divided. Some thought the Filipinos were savages and deserved it, others were horrified by what began to take place.
Eventually it became too much for even the Army, Google "Samar campaign" and "howling wilderness". At one point explicit orders were given by an American Army General to kill all male inhabitants ten and up. Much of this was publicized when a court martial was finally convened. Only the disobedience of subordinate commanders in NOT killing everyone someone mitigated the violence. (The initial order was pretty much literally to "kill them all", the concession to kill only males ten and up actually toned down the initial order and was seen as making it more humane...)
In the end there was a peace, and American colonialism took a somewhat light handed approach - schools and hospitals built etc. So much so that by the time of the Japanese invasion some 40 years later, the PI sided with the United States and fought convincingly against the Japanese. But... if you watch even the relatively period (1945) John Wayne film "Back to Bataan", it was widely acknowledged that the guerilla tradition and heroes of those times were something to be drawn on to once again inspire resistance.
