It depends on whether you mean the coach with the most wins (longevity stat) or the coach with the highest percentage of wins in his career. Paterno is the leader among active coaches in number of wins. Although technically he is no longer active as of end of 2011.
Highest win percentage will depend on how many seasons you set as the minimum for the stat. Obviously a coach could be 100% after 1 season, so it makes sense to set a bar of at least 5 or 10 seasons.
Bob Ford. University at Albany. Division 1-AA FCS
Knute Rockne with a record of 105 wins, 12 losses and 5 ties
Coach George Curry from Berwick is the winningest coach in PA history.
Bob stoops
Kenneth McKinney
jim drewery
NFL: Don Shula.
George Curry - Berwick
Which coach became the winningest coach in NFL history while with the Dolphins
1993 Don Shula Professional football Winningest NFL coach
Dan Reeves is the winningest coach in Atlanta Falcon history with 49 wins.
If by division one football you actually mean the Football Bowl Subdivision (at the time known as I-A), then FA Dry may be the first. He first became a head coach at Tulsa in 1972. That predates Willie Jeffries, who was the first African-American head coach at a I-A school, coaching at Wichita State in 1979. There have been many African American head coaches at the Historically Black Colleges and Universities, many of which are now at the Football Championship Subdivision (previously I-AA). Since Joe Paterno has had 111 wins vacated, Eddie Robinson is considered by the NCAA to be the winningest coach in division one football history, having started as the head coach of Grambling in 1941. Grambling is in the Southwestern Athletic Conference at the FCS level.