You can see the content of flagged comments by going into your profile settings and turning on the [showdead] option. Currently there are 26 flagged comments, so to pick a few random ones:
"By that standard, the only way to never do anything inappropriate is to never do anything."
"It's interesting that you construct a whole evil persona for someone..."
"When your worth is defined solely by how horny you make the opposite sex..."
"I cannot understand why sexual harassment takes such a toll on women. I've been sexually harassed by other men before, and somehow it wasn't as big of a problem..."
I didn't cherry-pick the above examples; they were just the first few that showed up with Command-F [flagged]. "Incendiary" is still probably the best way to describe these comments, which is why they're flagged. The other reason is shallowness on a controversial topic, which usually leads to flamewars.
If you see a comment that breaks a specific guideline in https://news.ycombinator.com/newsguidelines.html then you're encouraged to flag it. (You need a certain amount of karma to see the flag button.) The main reason that the comments you mention aren't flagged is usually because they don't violate any of the guidelines. The system isn't perfect, but it seems to work remarkably well given the size of HN's audience.
Regarding talking about downvotes, I understand and can relate to the point of view. To clarify, I didn't mean anything by the word "complain." The reason to avoid mentioning "downvotes" at all is because (a) talking about downvotes spawns low-quality subthreads almost instantly, and (b) it gives your comment an unfair advantage. HN's voting system fluctuates wildly thanks to the diversity of the people that now have the privilege of downvoting, but in general, high-quality substantive comments tend to rise.
If you want to give a few examples of comments you feel were unfairly flagged, or unflagged comments that you feel break the guidelines, I'd be happy to chat about those. (We're currently in a flagged subthread, so there's no harm in continuing our conversation.)
EDIT: To address one specific point more thoroughly:
An orthodox viewpoint can be written casually, unsourced, tinged with moral judgment, etc, and still get away unflagged and not downvoted. An unorthodox viewpoint will get ripped apart on the tiniest error, missing source, or mis-chosen wordage.
Unorthodox, controversial viewpoints are indeed held to a higher standard, but the reason is because it fosters better conversation. For these, HN is optimized for substantive-but-neutral. Deviating from either axis tends to produce flamewars of the worst caliber.