I came across this article...surprisingly. I'm guessing the didn't want the ACTUAL winningest active coach on there...?
http://wallstcheatsheet.com/sports/ncaa-football-who-is-the-winningest-a...
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Article says it's by winning percentage. Beamer's early years bring him down. Beamer's winning percentage over the past 20 years is .736, which would put him in the top 15. The most remarkable thing about Beamer is that he built a major program practically from scratch, which only two or three other active coaches can say.
Based off of win% instead of actual quantity of wins. Personally I associate "winningest" with most wins.
Touche...I just realized that. I also think that "winningest" means most wins...
"Winning percentagest" was what he meant to put in the title