It's most likely the stereo that is directly to blame but it's doing so to protect the speakers. If the bass would continue to increase above a certain point, it would either damage the speakers over time or the bass would start overpowering all other output sounds.
That said, you could try an aftermarket headunit and see how it sounds with the stock speakers. If you like the sound and it doesn't blow any of your speakers in the long term, you'll have what you want. If you don't like the sound or it does damage the speakers, buy yourself a set of aftermarket speakers that can handle the power and you'll be good to go.
Hatch Nation #13 : Rally Revolution #13 : ROTM Jan '13
It's Bryan, not Brian
RSVT-170 Build in Progress
Rusty is dead