Try reversing the polarity of the wires from the amp to the sub. The way it is now, the sound from the car is out of phase with the sub and it's reducing the level or it's loud enough that it's masking the sound from the sub. A car has its own noise signature and if you have a way to measure the car's response, you'll see that much of it is in the same range as your sub, which means the power to the sub needs to be greater than it is now because it's not able to overcome the car's sound. You can also try a lower Low Pass crossover frequency, to reduce the overlap. Since the car is already producing the frequencies between the new LP setting and the High Pass, you won't notice the lack out output from the system. 60Hz is a good starting point on the Low Pass and 120 is a good starting point on the High Pass. It doesn't seem to make sense when reading it, but in practice, it works pretty well.
What make and model of car?