Religion is a focus of men's loyalty and thus a competitor of the government and not to be tolerated in a Comunist society.
Immediately following the takeover the new government moved against the Buddhists and the Buddhists responded by ceasing to do much of anything. The country was collapsing precipitously because nothing was getting done. So the government relented and labeled B'ism as part of the cultural identity of Viet Nam and thus to be tolerated. By politically disabling B'ists the country deprived itself of most of its human capital.
Repression of Catholics was harsher and did not relent so easily because Catholics are a minority.However,in time, it was discovered that most of the business talent resided in the Catholic community. When the VCs(the popular word for government people in VN) determined that VN could not survive economically as a collectivized communist system the VCs got out of the business of agriculture, then progressively out of business in general(banks excepted). The country went from the edge of starvation to being a major exporter of food in a couple of years and acquired a thriving business culture. The Catholics were leaders in business and their suppression would abort the new economy so the pressure let up and Catholicism was proclaimed to be an "indigenous" religion. However, Catholics still have political disabilities, they may not enter government and Catholic villages are not permitted to be sites for any factories aand are not eligible for anything like water systems. A result is that the talented go into business instead of government.
The Protestant phenomenon is incomprehensible to the VCs. It cannot be defined as "native" and it is spreading very rapidly among the minorities who are already a despised group that has not been amenable to government dictates. They don't stay put and don't re-educate very well. And the minorities have no loyalty to the State or to the Country.
A result of the persecution of the Buddhists and the Catholics has been to end their mutual antipathy which the VCs had counted on to keep both under control. The Buddhists have learned from the Catholics how to do busines from a Judeo-Christian foundation and everybody is out trying to make a buck instead of studying the wisdom of Chairman Ho. This is not what the VCs had in mind at all, and the phenomenon is beginning to extend to the minorities. The Catholics and Buddhists are beginning to sympathize with the minorities and take their part and the minorities are losing their "despised" status which the VCs count on to keep them in line.