I believe that the jobs in question involved working for the “zionist” economy. Jobs such as working for international companies in technological areas, rather than jobs within the frum community (such as retailing, teaching, service base industries, manufacture of items retailed only in the frum community, etc.).
Thus what they were protesting was participating in the zionist economy. If one assumes that the current issues are actually a classic version of a “kulturkampf” (culture wars in which one culture will survive and the other will be forced underground or exteriminated), then such protests are reasonable. The issue is not how one will earn a parnassah, but rather whether Israel will be a Jewish state (based on Torah) or a secular state (based on western secular values). By this standard, working for the western secularists is as much a collaborator, as someone who, as an example, willing worked for the Nazis’ economy, was a collaborator.
The the Israeli have created a situation in which a large part of its population sees the “mainstream” as a mortal enemy is a serious problem, which is not addressed, dooms the Yishuv.