Well this one isn't.
People flag articles because they disagree with them, but also because they just think the discussion may descend into uninformative yelling. My point concerned the discussions that do appear, rather than which articles make it through unflagged, but even there it appears they don't support the narrative of "only good things about Israel appear in the media."
There's a relevant discussion in this recent post from a couple weeks ago:
Ask HN: Are we allowed to discuss Israel on HN?
https://news.ycombinator.com/item?id=44947788
"We want to give the topic of Israel and Gaza fair exposure, as it's obviously an important story and it would feel wrong to pretend it's not happening.
At the same time, every time we have one of these stories on the front page, it turns in to a hellish flamewar, we have to spend all day moderating it..."