Well it was a very prominent topic in my undergraduate experience. I can recommend Paul Kramer's The Blood of Government: Race, Empire and the United States and the Philippines. Its a well documented account of the period of colonization, the war, and the move toward independence. My guess is that it is often overlooked because of the fiat way that Roosevelt declared the war over two times despite continuing hostilities. There was a large effort to make the occupation appear benevolent and progressive. Recalling the works of Walter LaFeber and William Appleman Williams, I believe historians have often overlooked the war and instead focused on the importance of the War of 1898, the Roosevelt Corollary, and the Great White Fleet and the US' progression into a period as an international power. For these historians of American expansion or empire, the Philippines simply represented an anomaly in US foreign policy, since it was an actual colonization rather than hegemonic influence, and did not tie into the larger theme of US policy at the time. Obviously this is a problematic position, and Kramer does a great job of bringing the Philippines back into US history.

Edit: Paul, not Jim

You mean as in, why isn't it discussed more as a part of US History education?

How the American occupation of the Philippines is viewed in the Philippines varies wildly from school to school and from author to author. The works of Sonia Zaide were said to be pro-American (i.e. extols the positive consequences of the American occupation in the Philippines) while other more radical writers like Jose Marie Sison, who is a renowned communist supporter, stands by the assertion that the American occupation is what started the economic downfall of the Philippines.

Personally, I don't know how the American occupation is discussed in other universities, but many of the social science professors (history included) in the University of the Philippines discuss the occupation as a bane to the nation (despite the fact that the University of the Philippines was established by the US in 1908). Furthermore, the current relations between the US and the Philippines has always been a target of student activists. American influence in the Philippines has been linked to the rise in commodity and matriculation prices and the decrease in quality and quantity of public schools in the country.

I guess at its most basic level, the war is a footnote compared to the war that started it (the Spanish American War that itself receives little discussion). The biggest overall impact that the war brought was the U.S onto the world stage as a powerhouse/equal someone that Europe should have their radar on. The war in the Phillipines cost a few thousand soldiers lives, and more more Filipino lives, but it was a U.S victory to colony that was peacefully separated from the U.S after world war 2. I still think this war receives more attention than some other examples of U.S aggression like the U.S's almost consistent intervention in Nicaragua.

I could not agree more, while writing a paper for my Vietnam War class about the similarities between the conflicts I stumbled apon a great article "Two American Wars in Asia: Successful Colonial Warfare in the Philippines and Cold War Failure in Vietnam." by J.M. Gates which more then just talking about the conflicted talked about how it is discussed and portrayed. Gates makes some really interesting points about how he believes the idea most people have about the war is just wrong and how the war was actually less cruel then a lot of Historians would argue and goes on to talk about all the civil action we did down there and how in the end a large part of the population was glad to be under the United States. Lastly he ends with this interesting point about how hard it is to change how people talk about an event after the common idea of it's been the same for so long it becomes very hard to change that. Overall was a fantastic little read about the war, Vietnam and about how they were portrayed in History.