I hear you, but am not sure I have a good answer. There's simply no consensus about what belongs on the HN front page. It's a gigantic tug of war every day, and many users (on either side of any disagreement) feel bad when the content they favor doesn't prevail. It's good that people care, but it sucks that many are guaranteed to be disappointed. We don't seem to be able to eliminate that effect, only manage it and try to minimize it.
In the current case, it's important to realize that a post getting killed by user flags is a really strong signal. It's probably the strongest signal we get. That needs to count for something.
