The autopilot on landing follows the ILS path. These are standard frequencies that are "beamed" out from the runway to show the aircraft the ideal glide slope to follow (the localiser and the glide slope) The autopilot takes these signals and follows them down to the runway........that was the simple answer. As for your flair question, only if the aircraft has autoland, otherwise the system will fly the aircraft without flair into the ground. Pilots don't like as a rule giving this bit of control away and go manual shortly before touch down. However in this case, if the crew were flying an autoland approach and an RA is inop, then certain autoland options are also inop, throttle retard on touch down for example.
The RA was not inoperative, but malfunctioning. So, the throttle retard is exatcly what happened, but the plane was still high in the air, in stead of touching down.
I don't know about the visibility, but it didn't seem very hazy on TV, only a little. People driving on the highway could see the plane in the air, just before it crashed. The clouds were very low though.
Charley, at what altitude (above ground level) are you flying when lowering the gear?