Recent scholarship has re-examined the United States as an imperial power, bringing new insights about the dynamics of American power both prior to and after WWII. Certainly it was a colonial power, directly in places like the Philippines, Cuba, Puerto Rico, etc and an imperial power in Latin America.

Yet, anti-colonialism has been a prominent part of its rhetoric. This worried the European colonial powers. While in practice, many of the European empires grew even strong between the 1910s-1930s, the 'colonial consensus' weakened a great deal. By that I mean the idea that colonialism as a form of unequal rule was just and correct form of government. What did this? Certain key events like Woodrow Wilson's 14 points and talk of self-determination, the Russian revolution and Lenin's rhetoric about colonialism and imperialism, the mandate states after WWI (which acknowledged some European states were unfit to have colonies, thus interjecting a 'moral' element into colonialism), and inquiries by domestic governments in London and Paris into terrible conditions in the colonies.

This takes us to WWII. President Roosevelt/FDR was, albeit patronizing and by no means unbiased in views of colonial peoples, more liberal than the European colonial powers. Yes, America had the Philippines--but the US had instituted a Philippine Commonwealth government staffed by Filipinos and promised full independence. After 10 years, beginning in 1935 and ending in 1945, they would have full independence. FDR likewise envisioned trusteeship (monitored self-government followed by independence) as a good model of Europe's decolonization.

That was just plain bad for the business of the European empires. But they had to deal with an emerging US and the reality that they lost control over their empires during the war. And so, in 1942 Queen Wilhelmina went on the radio in the US and spoke of the Dutch commitment to colonial reform and expanding the rights of peoples in the Indes. Charles de Gaulle made a grandiose declaration in March 1945 that would transform the French empire into the French Union, awarding colonial peoples autonomy within it with local control over finances, government, and an army. Europe's empires knew that the colonial consensus was over. But they didn't believe colonialism as such also had to end. At the end of the war, both the Netherlands and France moved to re-conquer their lost colonies in Asia.

FDR would die, replaced by Truman who did not have the same zeal of trusteeship. He also dealt with the emergence of the Cold War, which placed competing and conflicting demands on US policy. The ideal scenario was to promote independence of the colonial peoples in a way that halted the spread of communism. However, rebuilding and protecting Europe was the paramount. And Washington needed Dutch and French cooperation to achieve their economic, political, and military plans. Both of these colonial powers leveraged their cooperation in American-led European affairs to the return of their colonial strength in Asia between 1945-1948. France would always have a stronger hand to play, as the bigger and more influential of the two.

Accounting for the different outcomes has much to do with the Asians leading the revolutions. In the Indies, where Japan had quickly overthrown the Dutch, two prominent non-communist leaders emerged quickly -- Mohammad Hatta and Sukarno. They however, did have communist rivals. Notable was Musso, a leader of the PKI communist party who had trained for several years at the Soviet Comintern. While the future Indonesians were struggling for independence, there was also a battle between Hatta and Sukarno's Republican government and the PKI communist party. In late 1948, PKI members staged a coup in the Madiun affair, prompting a crackdown by Sukarno (who, having been a leader under the Japanese occupation had far more support) that killed Musso and eliminated the PKI as contender. This was ultimately the key. In international negotiations during 1949, Sukarno could reliably speak of being anti-communist. He could portray his government, and not the Dutch, as both the rightful leader and the one that could halt any spread of Soviet influence. Allowing the return of the Dutch would only compromise that, and allow for a resurgence of the PKI.

The situation is completely different in Vietnam. While the Democratic Republic of Vietnam (DRV) and its Viet Minh front was led by communists early on, it had a sizeable number of non-communist groups as well. It's leader Ho Chi Minh, like Musso, had also trained at the Comintern and had organized the communist parties of Southeast Asia during the interwar period. However, almost from the start, the DRV's communist leadership began fighting with its rival non-communist nationalists. In 1946 Vo Nguyen Giap, with French support, attacked the military forces of the non-communists VNQDD, Dong Minh Hoi, and Dai Viet parties (at this point the French thought the communists were easier to negotiate with). The non-communist parties were removed from the DRV National Assembly too. In the south, powerful religious groups--with their own armies--fought with the DRV's leadership and eventually opted to work with France toward a gradual independence. At this moment, the now-exiled northern nationalist parties and southern groups agreed to support a new non-communist State of Vietnam government that would have a restrained independence.

In this way, the DRV government failed. Unlike Indonesia, they were too thoroughly controlled by communist party members, which made it highly unlikely to gain US support (though they tried very hard to downplay their communism to the international and domestic audience, for just this reason). When the DRV tried to form an anti-colonial front with these Indonesia revolutionaries, the first Indonesian PM Sjahir said: "Ho is also dependent on the support of the Communists ... if we ally ourselves with Ho Chi Minh, we will weaken ourselves and delay independence." Ultimately their diplomatic initiative failed, as Christopher Goscha notes in Un état né de la guerre (2012). The US would need France's support in Europe, and could stomach backing the non-communist State of Vietnam while pushing France to grant it genuine independence -- something that only happened in 1954.

Quote from: Hanna Papanek, "Note on Soedjatmoko's recollections of a historic moment," Indonesia 49 (1990).

/u/Lich-su already gave a fantastic answer, and I want to add that the government of an independent Indonesia agreed on in 1949 was the United States of Indonesia (Republik Indonesia Serikat). The following year, it was changed into a unitary Republic of Indonesia.

Over time, US concern over the influence of communism in the central government of Indonesia grew, and this led to covert aid of rebels in Sumatra (PRRI) and Sulawesi (Permesta). Among other concerns, these two rebellions were attempts to either increase regional autonomy or to secede altogether.

So it was not that the US government opposed the Dutch government, as much as it had very different interests w.r.t. the independence movements in the region.