Alpha is also called "Angle of Attack". It is the angle between the relative wind and the chord line of the wing. When the angle of attack is increased to a certain point, the airflow over the wing is no longer smooth. Turbulence is created after the wing, and it loses lift. This is known as a stall.
"Alpha protection" is a system which prevents the angle of attack from getting too high. This is done by software monitoring the plane's angle of attack sensor. When a high alpha situation is detected, the software lowers the nose of the plane to maintain high but still safe angle of attack. It also commands full thrust to all engines. This system is designed to prevent pilots from stalling the aircraft and to allow them to get the best possible performance in emergency e.g. in a wind-shear.
This is not part of the autopilot. It is integrated into the flight control computer and activated at all times. Autopilot are functions which fly the plane in a certain way to reduce the pilot's workload in normal situations (e.g. climb to 13,000 feet, turn left to heading 340).
Pilots can opt to turn off such protection systems should it malfunction, or a very special occasion exists where these protections should be switched off, such as performing at an airshow.
In the Airbus, the A320 was the first "fly-by-wire" aircraft. During a demonstration flight AF296 when showing off the alpha-protection system the pilots took the airplane too low and too slow and disabled the part of the system that should have commanded full thrust. The plane didn't stall but was having too little energy to climb anyway. It crashed gently into the trees.
In an acceptance flight, the pilots were testing the alpha-protection at low altitude. The system should have prevented the plane from pitching too high. However, to the surprise of the crew, it failed. The plane stalled with insufficient altitude to recover. The system did not work because water got into the angle-of-attack probes during previous improper washing procedure, froze during the flight and blocked the probes.
In AF447, the system switched to "alternate law" and no longer provided stall protection, because the pitot tubes (airspeed sensors) froze over. The plane stalled from 38,000 feet to the water after the pilots failed to apply correct procedure for unreliable airspeed.