Well, the most basic explanation is geography. Trade-oriented states are more likely to become Muslim, while agricultural states are more likely to retain Buddhism, Hinduism, or Confucianism. To prove my point, I'll reference 1) Islam in the mainland and 2) non-Islam in the islands:
- Champa, the most maritime-oriented realm of mainland Southeast Asia (because all ships going to or coming from China must pass the Cham coastline except for ships to/from Manila and Nagasaki) with a relative paucity of good agricultural land, was also among the few areas in the mainland where many people turned to Islam. Arakan, another coastal kingdom, also had a large Muslim population. Thailand, the most maritime-oriented of the three main kingdoms of Early Modern mainland Southeast Asia - by the early 19th century the majority of government revenues derived from trade - was also the kingdom with the closest contact to the Islamic world; King Narai emulated Persian architectural styles and even cuisine, while in 1686 Muslims in Ayutthaya launched a revolt and held out for several days against massive opposition. Sultan Ibrahim of Cambodia is well-known, of course. These are unprecedented in more agricultural Vietnam. It's also important to note that in the mainland, the main ports were held by agricultural kingdoms with a few exceptions (e.g. Ayutthaya by Thailand, Pegu by Burma, Hoi An by Vietnam).
- In South-Central Java, conversion was slow (Islam was probably only widely present among the general population by the 1630s), involved more conquest than was the case in the more pacific, voluntary conversions of the ports, and was much more syncrestic - a "mystic synthesis," to quote the main historian of Java. For example, major Javanese kings who were proud Muslims also went on pilgrimage to speak with the Goddess of the Southern Seas! Javanese chronicles generally consider Islamization to be much less important than Majapahit's collapse, and for good reason. Javanese millenarist movements drew less on the Mahdi and much more on the prophecies of King Jayabaya, who ruled in the 12th century, while some colonial-era Javanese chronicles even blame Islam for forcing the native gods of Java to "retire into concealment" and thereby ruining Java. Bali and its Javanese offshoots, of course, never bothered to convert. Makasar in South Sulawesi, another wet rice region, also did not convert until the early 1600s.[1]
So why Islam? The reason is that beginning in the 14th century or so, Arab, Persian, and Muslim Indian (Gujarati traders, for instance, were generally Muslim even if Gujarat as a whole was not) merchants became much more common in the region. So we first have a situation where "the king is a pagan; the merchants are Moors."[2] Muslims prefer ports with Muslim facilities, and especially ports with Muslim rulers. So a Buddhist, Hindu, or animist king might decide to attract Muslims by building mosques, then by appointing
qadis, and eventually we have full-on conversion as the conclusion of a gradual set of concessions to the Muslim trading community. But if an obstinate king refuses to give concessions to Muslims, those Muslims are fully willing to visit ports ruled by his more congenial competitors and, in certain cases, even militarily support him like Muslims supported Aceh against the Portuguese. So the competitively commercial nature of Archipelagic politics incentivises Islamization. By contrast, the Chinese did not care nearly as much about whether there were elements of Chinese culture in the ports they were visiting.[3] Hence Thailand to this day remains much less Chinese than Aceh is Muslim. And once the coast is Muslim, the agricultural inland becomes more likely to become Muslim (as in Java). Not only that, Islam encourages political centralization for chiefs who want to make the leap to being a king; a 1544 Portuguese report notes that before Islam, the Malukus did not have writing, laws, coins, gongs, daggers, and "all the other good things [the Malukuns] have."
TL;DR: Trade gives incentives to convert, and once the coast is Muslim the agricultural inland is also likely to take up a syncretic (or "watered-down") Islam. In the mainland there was less trade and ports were better held by agricultural states, hence less conversion.
[1] Admittedly this may have more to do with the political landscape and ideology, e.g. how South Sulawesi kings claimed divine descent less compatible with Islam.
[2] This is how a Portuguese described Brunei in 1514 but must have applied to most now-Muslim ports at some point in their history, like Aceh/Semudera in the late 13th century, Melaka in the early 15th century, or Makasar in the late 16th century.
[3] If the Chinese followed a missionary religion like Muslims, Thailand would definitely have converted in the 18th century.
