It seems hard to believe now, especially after Ceausescu clung by his fingernails to power while the rest of Eastern Europe turned away from Communism, but during the seventies and eighties he had a reputation as something of a pro-Western (or at least not stridently anti-Western) "reformer" who worked hard to cultivate ties with the United States, Britain and other non-Communist powers.
His own propaganda films made sure to show he and Elena hobnobbing with the likes of Richard Nixon and Pierre Trudeau, and riding in Queen Elizabeth's carriage. Meanwhile, Romania entered into seemingly lucrative business deals with Western nations, like building French Citroen automobiles under license and buying aircraft from Britain (and then trying to pay for them with strawberries). They even sent a team to the 1984 summer Olympics, defying the Soviet-led boycott.
I'm not so sure about his country's ties with Israel, buy they would appear to fit this pattern.
In his book, Red Horizons, Ion Mihai Pacepa - who, until his defection in 1978, was the # 1 of the Romanian Securitate - alleged that Ceausescu literally sold the right of Romanian Jews (and Germans) to emigrate to their respective governments, in exchange for hard currency. And I think that like Yugoslavia, with whom Communist Romania enjoyed friendly relationships, the country generally pursued a somewhat-independent foreign policy; for example, Romanian athletes didn't boycott the 1984 Olympics and due to the country's relatively liberal stance (mainly a façade), the U.S. granted favourable loans to what was seen as a potential mole in the Eastern Bloc.
These loans, however, had to be repayed and this is one of the reasons as to why Communist Romania was forced to export much of what it produced, leading to the shortages in the '80s. If Pacepa's allegations are to be believed, then the Ceausescus did almost everything in their power to get hold of cold, hard cash.
I'll give you a straight answer, with a little less speculation:
Part of it was down to posturing West. Romania sought to establish a sort of independence away from the rest of the Communist bloc, and avoid the negative spotlight on others in its bloc. It thus was seen more positively in the West. At the same time, it benefited handsomely too because it was able to avoid condemnation from the Arab states and maintain relations with them, while still recognizing Israel, and it benefited from bilateral cooperation with Israel as well.
For a few years, for example, Israel helped Romania with agricultural development, until the agreement was frozen. Despite the advances made, Romania chose to freeze the cooperation. Yosef Govrin, a former official in the Israeli Foreign Ministry (and ambassador to Romania for 4 years), speculated that this might have been because Romania feared that their agriculturalists would run away and stay in Israel when brought there to learn, or that they would criticize their own work systems after seeing the Israeli work systems.
Other reasons speculated on include that perhaps the Soviets wanted to keep at least one satellite in contact with Israel. That would, presumably, provide them with the ability to have intelligence contacts in Israel, even if not through the Soviet Union directly. While this is possible, it doesn't explain why Romania in particular, and many other facets, including the cooperation that continued elsewhere as I mentioned.
Israel's ability to serve as a conduit for better Romanian-US relations, as mentioned, was undoubtedly important. But another aspect (besides the prospect of defense and tech cooperation with a growing Israel) was the Israeli-Romanian population, estimated to be around 400,000. Romania hoped to tap into this community, bringing some of them to study in Romanian universities (which were more accessible in terms of admissions) and also to cultivate ties with Israel in general through them. They were considered fairly influential, and could pose a good source of tourism revenues for Romania as well. Plus, since many of those Jews were in Romania at one time, the two countries had a cultural connection to some extent as well.
So to sum it up:
The Soviets may have had a reason to allow it, if not encourage it, in the form of maintaining an "in" with the Israelis.
The Romanians benefited handsomely from a state that was gaining more in advanced technology, in later years mostly.
It provided diplomatic cover and a sense of independence and pride for Ceausescu, who was able to maintain foreign relations with Israel and the West while also the Arab states, and have diplomatic neutrality in that issue in particular.
The Romanians could tap into shared cultural ties with Romanian Jews in Israel and remaining in Romania for a source of tourism and influence in Israel, while looking for an "in" to US-Israel relations transferring to better US-Romania relations.
Those are the main reasons. Enjoy!