To understand why Israel keeps targeting UNRWA infrastructure and UNRWA workers (and by extension, human rights activists) aside from the accusations they're ~secretly Hamas~, we must put it into the context of which these organisations operate.
To put it lightly, Israel is not a fan of international NGOs and human rights organisations at all, but especially the ones whose existence revolves around advocating for Palestinian rights and exposing the crimes of the occupation. It is not a fan of Palestinian ones at all either, but that goes without saying. I would even suggest that Israeli organisations like "Breaking the Silence" and "BtSelem" fall under this category, even liberal ~coexistence~ type groups like "Standing Together" are seen with suspicion to a degree as they pose a threat to the status quo. The Israeli state and Zionists also see the work of such organisations as a method of "delegitimising Israel" and "singling out Israel" and so on. There is even a pro-Israel organisation called "NGO Monitor" which exists to combat this exact thing.
In the case of UNRWA, there is a specific criticism made by Israel against them (aside from the secret Hamas operative one), and that is they "indoctrinate" Palestinians to hold onto their right of return by perpetually keeping them refugees. Obviously, it's a silly argument that is not worth entertaining. There are a lot of genuine criticisms to be made about UNRWA (which is largely to do with the NGOisation of the Palestinian struggle but that's another post) but they have helped sustain Palestinian existence and livelihoods by providing aid, employment, education and so on. In times of war and crisis, UNRWA has been providing important aid to Palestinians. It's hard not to see Israel's attack on UNRWA as an attack on that.
Even groups which are headed by Palestinians, both in the diaspora and in Palestine, such as International Solidarity Movement (ISM) or Youth Against Settlements, face constant attacks by settlers and soldiers. The purpose of these groups is to demonstrate civil disobedience and resist the occupation non-violently yet still face violence. Others exist merely to just document.
Israel is also so used to operating with impunity that any organisation shedding light on Israel's atrocities against Palestinians is a blow to their propaganda. All the reports, documentaries, and findings produce evidence that then becomes hard to deny or hide. There is a reason why Israel is currently not letting in any journalists or aid workers into Gaza, and even the ones it is letting in it is targeting as we've seen time and time again over the past year.
The problematic nature of NGOisation and the apoliticisation of the human rights framework aside, many of these organisations have played a role in presenting the case of the Palestinian struggle in front of a world audience. The ability to not just document or advocate but be believed is a privilege Westerners have and that's where these organisations tend to come in. As long as these organisations exist and/or have a reason to be in the West Bank and/or Gaza, then Israel cannot do what it actually wants to i.e. constant settlement building, attempted ethnic cleansing and more importantly, trying to convince the world that Palestinians do not have a justified struggle against the occupation and the allegations against Israel are merely "false."
