If I recall it may have been because there was already a rebellion going on in Cuba against the Spanish. Sending in troops to help their war of independence was the reason given for America to throw its hat in the ring in the first place.

This didn't mean Cuba was altogether independent, as it was the United States forces that negotiated the treaty with the Spanish after on behalf of the rebels, and they refused to let the rebel forces enter the capitol until they agreed to adopt a constitution written for them by the Americans. Not to mention, Cuba was unable to sign any treaties with other countries, and Guantanamo Bay was to become American. To me, Cuba seemed like a kind of proto-neocolony, with formal independence, however its foreign policies as well as its industries would be under the hegemony of another country or another countries' business elite. This would basically be the same basic model for all former colonies after they were ceded at the end of the world wars.

I think that the reason Cuba was given formal independence was because there was already a nationalist fighting force in full momentum at the time of US involvement. It probably would have been costly to have to police a country as a colony while much of the population was already in full flex independence fight mode. If the US is going to have control over their exports, have the power to take command of their military, have the final say over their foreign policy, why have to fight to keep it a colony?

Some posters have already pointed out the situation with Cuba already having a long active independence movement and being in rebellion against Spain and the ostensible reason for U.S aggression against Spain being in aid of that movement. It would be unseemly for the United States to fight a war predicated upon aiding the Cuban independence movement and then occupying it. However, as has been rightly pointed out already, the United States did reserve certain rights to effectively be suzerain over Cuba (the Platt Amendment, jurisdiction over Guantanamo Bay, etc.)

The Philippines in many ways was an unexpected gain for the Americans in the war and they correspondingly did not have a plan for it in the event of occupation. It was quickly determined after the war in a government report that the Philippines were not yet ready to govern themselves and that they required the United States to be a civilizing, Christianizing (even though the Spanish had introduced Catholicism) force for the hapless Filipinos. Indeed President William McKinley himself makes reference to this notion. Further, the Philippines were a tremendous boon to the United States in its quest to obtain a presence in the Pacific by which to facilitate trade in China. It played to both the commercial interests of business at the time and the imperialist sensibilities of some in politics who believed that the United States should take an active and aggressive role on the world stage.