That's wrong. Both the flamewar detector (a.k.a. the overheated discussion detector) and user flags do that, and there are other software mechanisms that do it too. For example, if a story has been on the front page for more than (IIRC) 18 hours, it gets an automatic downweight unless we manually override it.
Also, keep in mind that user flags affect a submission's rank long before the [flagged] marker appears.