The mods (& many users) like to flag anything that could be "controversial" or lead to "flame wars". It's possible they thought that article could get people "fired up" and it could result in "arguments" in the comments. And this doesn't just apply to stories - if you have an opinion that the mods or some user doesn't like, you'll be accused of posting flame bait.

This "community" (as the mods like to call it) is really a business tool for YC. Attract nerds to the site, funnel them into the YC program, make startups, collect billions. If this was your money-making tool, you'd probably want to quash all controversy too.