I used to work at a stereo shop in Norfolk and would see this friggin ALL THE TIME!!!! Normally kids not knowing anything about systems trying to bump with the big boys and screwing it up. Not to say that you did, of course, but it was more then a common occurrence.
Anyhoot, if your getting the protection light and have 12v there I wouldn't worry about fuses or ground. it's going to more likely be dealing with the amp itself, normally something stupid. Depending on the make of the amp it could be a couple things.....
Anyway, here's a couple things you can try...
First is to check the Remote wire (normally blue) coming from the head unit, this should have very nominal voltage when the radio is on.
Turn the radio off and check the voltage of the blue wire again. if it still has voltage there could be other issues.
Next, mark your amp or take note of where the settings are, Gain/Low/Med/High etc... then turn the gain down to 0.
you might have to turn the radio off then turn it back on... to get it to take. This should make your protection light go out as the amp is not putting anything out... if the protection light does go out, SLOWLY start turning the gain back up trying to get it to the point of where the protection tripped the first time. if it lets you get to just under the level that if first tripped at then it's going to be an actual component in the amp, more then likely the power supply, that is "failing". If you can soldier, then it's an easy fix, radio shack should have something that would work.
(I have also seen where if the speaker wires become grounded this can happen as well, so take a look at those too.)
Can you explain your setup? Like how old the amp is, the head unit, so on...
Hope this helps. I'd come take a look at it if I could but for now it's strictly Web Wheelin for this guy.