During the years before and during WWII, Japan was horrifically cruel to both the people in land they captured (e.g.: Filipinos, Indonesians) and the enemies they were fighting (e.g.: Australians, Indians, British). You would think that, with all the atrocities and crimes they committed, Japan would be hated by everyone right now.
And yet, with the exception of Korea and probably China, almost every country sees Japan in a pretty positive light. They rank high in popularity charts, tourists love the place, and many associate Japan with good values, like respect and loyalty. Japan also has amicable relations with most of the globe.
Why is this?
Specifically addressing Indonesia, many of their independence leaders collaborated with the Japanese at various levels. Sukarno the first president was used as a nationalist figure to stoke the flames of pan-Asian anti-European colonialism and to muster support for Japanese war efforts. So much so that when he was pressured to declare independence at the end of WW2, he initially refused to do so without explicit Japanese support. In the end, the proclamation of independence was read at the house of an IJN rear admiral.
On Japan's side, at the very least several hundred IJA soldiers fought on the side of republican militias (many of which were founded and armed by the Japanese as potential auxiliary forces in case of Allied attack on the region) against the British and Dutch forces who came after WW2 to re-establish Dutch colonial rule.
All that is not to say that Indonesia was a puppet state of the Japanese, far from it, but rather that many of its earliest leaders were supported by the Japanese. Following WW2 as Japan's economy rose, the Japanese gave significant foreign aid and war reparations to Indonesia. At the same time, Indonesia was a huge market for Japanese goods and thus was an important export market for Japan, particularly in the 70s as anti-communist Suharto consolidated his power and brought Indonesia under US orbit.