We can debate the usefulness of the term apartheid to no end, but it's a fact that Palestinians in the West Bank are subject to Israeli military courts, whereas settlers and other Israelis retain the benefits of civilian courts.

Israeli settlement is counterproductive for Israel as well. Weakening the legitimacy of the internationally recognized representatives of the the would-be Palestinian state increases the likelihood that Palestinians will gravitate towards support of more extreme actors. The thought process can be summarized as follows: I am subject to violence by the Israelis, who do not respect our legitimate representatives, who have renounced violence, the denial of the right of Israel to exist and which even cooperates with Israel on some security matters. Notwithstanding the corruption of the Palestinian Authority also impacting its legitimacy, the Israelis make the international situation worse and contribute to an upward spiral of violence.

None of what I have said should be taken as an endorsement of violence or a dismissal of Israel's right to security. However, Israel's salami slicing of territory which was supposed to be reserved for a future Palestinian state, their implementation of a military justice system conferring fewer civil rights on Palestinians than Israelis occupy the same territory and their excessive use of violence in an often punitive way clearly shows that Israel is not an innocent victim of aggression in the conflict. Israel is also an aggressor and contributes to its international reputation as an oppressor.

So you may not like the characterization of Israel as an apartheid state, but its behavior towards the Palestinians lends itself to such a characterization. The conflict will continue forever until one side completely pushes the other out or both acknowledge their part in preventing the establishment of more peaceful relations and, hopefully, an end to the conflict.