The Portuguese did not colonize Indonesia, they merely set up some trading posts. So they had very little opportunity to catholicize more than a handful of Indonesians, especially since they were there only briefly (the Dutch kicked them out in the early 1600s).

Like the Portuguese, the Dutch originally did nothing more than build trading posts (and massacre some people if they felt it benefited their trade). Converting Indonesians to Christianity was never a priority for them. In fact, it was discouraged as spreading the gospel in areas with a large Islamic influence was, rightly, considered to be more trouble than it was worth. Only some remote areas that had a large Dutch presence and no muslim influence converted, such as the area around Manado and parts of the Moluccas.

Even when the Dutch started colonizing the entire archipelago in earnest, in the late 19th century, the policy of only allowing missionaries to work in areas where Islam had not yet penetrated persisted. Very few of these areas existed and they were divided up roughly equally between protestants and catholics. As a result Indonesia nowadays has some catholic enclaves (the island of Flores in the lesser Sunda islands, for example, or the southern half of West Papua) and some protestant ones (the Batak highlands and the northern half of West Papua, for instance). but for the most part is muslim.

The Portuguese ruled Indonesia too shortly and the Dutch Protestants didn't care about the spread of religion at all, they were only concerned with trade. They didn't even impose their own language and Dutch people who went to Indonesia had to learn Malay (Indonesian). The Spanish, one the other hand, thoroughly christianized the population of the Philippines and destroyed most traces of Islam, so that today Muslims are a small minority only in Mindanao.