Edit: here's an example on the front page right now: https://news.ycombinator.com/item?id=8461304.
The intention is not to suppress an important topic but to hold the countless me-too posts at bay—the ones that don't add anything significant. When the massive wave subsides, we'll remove the penalty. For example, there was a period where HN did this for NSA stories, but that hasn't been the case for a while.
From the HN Guidelines: "If they'd cover it on TV news, it's probably off-topic."[1] So if it's just an article like "2000 more people died of ebola in Liberia today" or "one more person was quarantined in Dallas", then it will probably get flagged (especially if it's the 13th article with a similar headline). If it's more hacker-related, like "mathematical models for predicting the ebola epidemic", it might have a better chance (as long as it's not the 13th article with the same headline).