Stories like this often get flagged because they devolve into political/religious flamewars. I think many people might have a knee-jerk reaction to posts about the Israel/Gaza war and flag them, because support for Israel vs. support for Palestine can be quite polarizing and emotional.
Not saying it's right or wrong, or that this sort of article is or isn't interesting to HN readers. But a reasonable reason for flagging an article is a belief that the topic at hand doesn't lend itself to thoughtful, interesting discussion.