Think of featured files as editor's picks. Just because a file has a high rating and lots of downloads it does not mean the file will be featured. You can find this type of file by ordering by downloads or rating. The featured file system works by moderators going through the gallery and any files they feel are exceptional (not just good but amazing) they will feature.
The system is subjective rather than objective; We have a system where if a file has a certain amount of downloads and a certain rating it will be put in a feature validation queue where a gallery moderators will go through the queue and feature any files they feel are exceptional. However, this list is there to notify us of anything we have missed not to set a criteria. Just because your file gets on this list doesn't mean it will be featured.
We once had it so that the whole system was objective and it was based on the gallery statistics for the file. However, this did not work thus we changed it to the new system which is much more effective.
If you feel your file should be featured and it has over 5 favourites or a rating of 4 or more you can submit it directly for moderator approval by using this thread. However, as the thread says you can only do this once per file and submit 5 files per month maximum. The decision is also final.
Please don't be disheartened if your file is not deemed to be feature worthy. It is the best of the best that get put in this category, by featuring all files it would devalue the purpose for its existence.