Israel is a small country. When Israelis are killed in terror attacks, everyone waits fearfully for names of their relatives and friends to be announced.

In my own case, which probably is typical, this fear has been justified more than half a dozen times. It happened again last week, in Thursday’s attack on the Merkaz Ha-Rav Yeshiva in Jerusalem. One of the boys killed was the 15-year-old grandson of a man I know well. He was the third generation in his family to study at the Merkaz Ha-Rav, from which both his father and grandfather had received their rabbinical ordinations. In the press reports on the murder of its eight students, the Merkaz Ha-Rav has been referred to as the “flagship” of the modern Orthodox yeshiva world in Israel, the implication being that it was a particularly symbolic target. There is a large measure of truth in this, for the Merkaz Ha-Rav is not only, as the press has pointed out, an elite institution that was the ideological birthplace of the religious settlement movement in the occupied territories, it also was the creation of a man who, more than any other in modern Jewish history, made such an ideology possible.

This man was Rabbi Abraham Isaac Hacohen Kook (1865-1935), the first chief rabbi of Palestine during the period of the British Mandate and — although his work continues to be little known to the general Jewish public — one of the most important 20th century Jewish religious philosophers.

It was Kook who founded the Merkaz Ha-Rav in 1924 as the first yeshiva in Palestine with a Zionist orientation, for which he was bitterly attacked by an anti-Zionist ultra-Orthodoxy. And it was he who imbued this yeshiva with an outlook that, more than 30 years after his death, was to transmute itself, under the influence of his son, Rabbi Tsvi Yehuda Kook, into Gush Emunim, the organization that spearheaded religious settlement in the occupied territories in the late 1960s and 1970s and from whose ranks much of the settlers’ subsequent leadership emerged.

Kook was an unusual combination of a mystic with kabbalistic leanings and a religious humanist who believed that there was a place for modern life and science within Judaism, which needed to be open to contemporary ideas and currents.

But the most unconventional aspect of his thought, from the perspective of traditional Orthodoxy, was his viewing secular Zionism as a movement serving religious ends and even impelled by unconscious religious motivations.

For Kook, every Jew had within him an aspiration to holiness even if he himself was not aware of it; the left-wing, secular Zionist ambition of building a new Jewish society in Palestine based on physical work, social justice, and economic equality seemed to him, in its striving for a better world, a deeply spiritual undertaking that was hastening the Messianic age. The day would come, Kook held, when Zionism would realize the false nature of a secular consciousness and return to its full Jewish roots. Meanwhile, religious Jews should support it, chiding it when necessary for its anti-religious excesses but never forgetting that it was doing God’s work.

All this may seem theoretical. Yet what Kook did was to provide a powerful intellectual justification for religious Jews to cooperate fully with a secular Zionist establishment — and when this establishment created, after his death, a secular Jewish state, to regard the latter and its institutions as part of a divine plan for Redemption that it was a religious commandment to support and take part in.

As taught at the Merkaz Ha-Rav Yeshiva and the many emulations of it that sprang up, this became the accepted outlook of what is known as Israel’s “national religious community,” which today comprises some half-million Jews or one-tenth of Israel’s Jewish population. And when, after the 1967 war, the territories occupied by Israel in the biblical heartland of Judea and Samaria became available for Jewish settlement, it was also this outlook that impelled Gush Emunim to co-opt as much of the Israeli state’s power as it could in order to settle Jews in these areas. The fusion of state power with religious idealism seemed perfectly legitimate from its point of view.

But what the leaders of the religious settlement movement failed to realize at the time was that the same state power that could be put to use by them had a will of its own that also could turn against them. This was what happened in the disengagement from Gaza in 2006, bitterly opposed by the “national religious” community, and it is what is threatening to happen on a much larger scale in the West Bank.

Today, this community, particularly its youth, feels betrayed and abandoned by the secular state it once championed, and increasingly alienated from it.

The murder of the eight students at the Merkaz Ha-Rav Yeshiva cannot, of course, be directly blamed on Israel’s secular government; if anything, the yeshiva itself was negligent in not posting guards and taking sensible precautions.

But the “national religious” community’s enraged feeling that it alone today in Israel is fully committed to the war against Palestinian terror, in which its government is at best half-heartedly engaging while continuing to pursue the mirage of peace negotiations with the Palestinian Authority, will only be strengthened.

The Kookian vision, which (however far it may have strayed from Kook’s original intentions) has served as this community’s guiding light for 80 years, is now foundering and close to collapse. Needless to say, the Palestinian gunman who chose the Merkaz Ha-Rav as his target was unlikely to have been aware of all this. He did not know the half of what he was shooting at.

Mr. Halkin is a contributing editor of The New York Sun.