Well, your car may be different. But in my car, if I put my amps under the seats, there would be the following problems:

1) Rear seat passengers would bump them with their toes.

2) Passenger legroom is reduced, see #1.

3) They would be more suceptible to damage if the car developed a leak and the floor got wet (happened in my GTI).

4) Amps would be visible from outside the car, making them more of a target.

Again, like I said, your car may be different. But in my car, the trunk is still the best place for them.