Could you give some concrete examples? Articles can get dropped off the front page when many people click the flag link (i.e. it's not always driven by the moderators). Also, I believe submissions with a high comments to up vote ratio are weighted down (the rationale being that it usually signals a controversial topic prone to flame wars). There have been cases of questionable hell banning, but this can usually be resolved by contacting the mods privately AFAIK.