What make and model sub(s) do you have? But to start off disconnect the sub(s) from the amp, turn it on and see if it still goes into protection mode. If it dose disconnect the RCA's (use caution do not touch the rca's to metal or one another) as well and see if it comes out of protection mode. Post your results.
I have 2 DEI Comp-X 12" ..... the amp is the factory modified BMF-1000D. I just removed the rca's and still in protection, then I removed the speaker wire, and still protected... I waited about 3-5 min. in between each to see if the light would change over. I then unplugged my remote wire and ran a jumper from the remote to 12+ to make sure it wasn't that. After that it still did not change... after doing all of this I connected everything back together and the amp turned on after 1 min. I really am confused now.. I started my car and again the amp was back in protection... I tested a few things listed above again and it seened to turn on fine with the key turned back and when I started the car it would become protected... My cap. is reading 12.4 with the car on accessory and 14.4 running as usual... I finally turned the amp upside down and took the back off and there was no sign of burnt wires or componants inside.... after I put the back on I started my car and the red light was still there, I lightly knocked on the bottom of the amp with my nuckles and I heard a click inside from the protection disabling and the green light came on and ststem turned on. It seems to be a interal prob. but I still have not idea why. I shut off the car and turned it back on and back to the red light again.... I'm very confused as I have never had a problem with this amp/ set-up ever and have had it for around 3 months in without removing anything... (sigh......)
Sometimes amps (and other equipment) simply break. Sounds like you may have an amp that is worn out and needs repair.
I agree with DYohn, if you have unplugged both the RCA’s and the Subs then it’s an internal problem inside the amp. Either take it in for repair or replace it.