Yes, the Romanian Communist Party (PCR) largely tolerated religion but there are some differences between different denominations. In short, they tolerated religion, but not every type of religion.

PCR came to full power on 30th of December 1947 when King Michael was forced to abdicate. He was the last check against communism and after his abdication the party controlled the entire country. At that time, Romania was a Orthodox majority country but with significant catholic and Greek-catholic minorities, plus some Muslims in Dobrogea and some neoportestants here and there.

Starting since then, the party started to directly intervene in religious affairs. The first years were indeed marked by many arrests of priests and theology students (theology students tended to support the far right during the interwar period and the early 40's) but there were differences along the road and some explanations regarding the attitude of the regime.

I will mostly talk about the attitude regarding the Orthodox Church (BOR) and then al little bit about the Greek-catholic one.

First let's get to the latter, the Greek-catholic church. It was widespread in Transylvania and was the results of the Habsburg Empire's strategy to convince some Orthodox region to at least accept the pope as the head. They were partially successful in Transylvania as a part of the Romanian ethnic group accepted this. While until the union of Transylvania with Romania the two Romanian churches did not go into open conflict because they were more concerned about the process of maghyarization and awakening national ideas in the Romanian mindset, but there were tensions. The communists were happy to kill two birds with one stone: attract the goodwill of BOR and finish off the Greco-catholic Church because their ties with the Vatican were seen as ties with the west (this was also why the party was not found of the Catholic church was or neoprotestants). They arrested numerous Greco-cathiolic priests and all of the leadership. The leadership was given the chance to crossover to Orthodoxy or stay in prison. Meanwhile, BOR started taking over Greco-Catholic churches and the number of followers fell. The exact number is difficult to know because censuses done during communism did not show religion, but in 1930 there were 7,9% of Greek-catholics and in 1992 (the first post communist census) there were 0,9%.

Now about the Orthodox Church (BOR). BOR was in a difficult position during the early years of communism because of two reasons. Firstly, the obvious aversion of communism towards religion and secondly the stance of BOR regarding the far right movements in the interwar period and it's support of the Antonescu regime and the war against USSR, plus the involvement of some church officials in the Holocaust (and the general discourse against the Jews). Romania being a very religious country, it would be unwise to discredit BOR too much. That went well with the idea of "symphony" that Orthodox Churches had. It basically means that the church is always close to the state authorities and tries to reach a modus vivendi. Overall they did just that with some "help". Patriarch Nicodim Munteanu (1939-1948) died at the right time and was replaced with Patriarch Justinian Marina. Marina is sometimes called the red patriarch and was close to the communists since a few years back. Since then, the Church did not criticized the regime, not even when some priests (even some in the higher hierarchy) and theology students were arrested, nor when entry to universities was almost impossible if your father was a priest(that lasted only in the 50's, just like the arrests of priests). PCR on it's part brushed aside the church's stance regarding the far right, it mentained the theology departments in universities and even contributed to church renovations and even building new ones.

The 50's were indeed some difficult years because of the arrests but also a time when Gheorghe Gheorghiu Dej inspected the restoration works at Neamt monastery and ordered that the pace should be quickened, for example. After the rather difficult first decade, the pace of arrests in general was eased and in the 60's the party started to shift it's focus on surveillance of the population rather than open repression as every major group that could pose a threat was eliminated and the collectivization campaign was finished. Since then, BOR enjoyed a surprisingly good life. It's leadership was close to the party. This link shows some high ranking priests with the party leadership. Patriarch Teoctist (1986-2007) was a member of the Grand National Assembly (the parliament) since 1975. The president of Romania (so Ceausescu) officially sanctioned the naming of new church heads in different regions and as it is the custom during services, the priest prays for the country leadership, thus the "let us pray for comrade Ceausescu" was a part of the service. The party closely supervised the elections of new church leaders and different people in the PCR leadership had different favorites.

BOR was mostly free to go on with their church services, their custom of going to every door during Epiphany, after the ban regarding being accepted to university for those who had "unhealthy origins" was lifted, sons of priests will be received and attending the Church seminars and studying theology at university level was tuition free. The anti-religious discourse of the 50's in propaganda was also toned down. The regime indeed banned religious classes during school and high school and important holydays (like Christmas or Easter) were not state holydays and thus you needed to go to work then. Father Christmas war replaced with Father Frost (of Soviet origin) until the end.

I will only mention briefly the fate of neoprotestant denominations. Their activity was always restricted and they never had official places of worship and they could only smuggle religious materials. The main reason for this was that they were American denomination and they never accepted US influence.

I will end with some info about the Orthodox churches (the buildings itself) during communism. There were around 12.000 churches, monasteries and other places of worship. More than half were repaired, restored or repainted during communism and the state gave money for many of them. There were also more than 500 (I do not know the exact number) of new churches being build. There were also some who were torn down but the vast majority were demolished when an entire neighborhood was torn down and rebuilt with communist housing blocks. Around 20 were demolished in Bucharest after 1977 when the regime started extensive works there (the well known People's House was stared to be build during this time) but some were saved by being moved away on rail (pic here) to a safe place. This means moving the building for a short distance so it will not stand in the way of a new road (or the older one who was enlarged).

P.S.: This is a good book that has a chapter about how the regime brushed aside the church's involvement in the Holocaust: The Romanian Orthodox Church and the Holocaust - Ion Popa