This is a lot like baseball pitching machines and balls getting scuffed up/ruined. It all comes down to the quality of the ball.
More expensive, higher quality leather balls fare far better in pitching machines, regardless of whether it throws baseballs or footballs. I would recommend at least a medium price level Wilson all leather ball (not synthetic leather).
One Final Note: Keeping your wheels clean, ridding them of abrasive substances (mud/dirt), will also go a long way toward keeping your footballs in good shape.