It's because people want to play as real teams. When you have one option what else are people going to play. As good as NFL 2k5, its not new and fresh.
It's just human nature to want something new and that's Madden. At the same time it's the only NFL game in town. If you want to play as the bears you can't in APF.
Let's say APF had perfect gameplay and more features than what was released, it still could not compete with Madden because we want an NFL game.
That said APF hurt themselves by releasing releasing a game that was practically a demo of APF 09.
Maybe APF will offer a fully customizable game and people like Finn, Puja, Dan create APF:NFL. That would be sweet.