Fair catch or not?
 

If a member of the receiving team signals for a fair catch, and his team member makes the catch instead (one who didn't give the signal), by rule is this a fair catch. We know the ball is dead, but does R still have the fair catch options such as lining up for a free kick?

The ball is dead but it's not a fair catch- thus no options.

NF 6-5-3

"...If, after a receiver signals, the catch is made by a teammate, it is not a fair catch but the ball becomes dead."

I also believe that this player is not afforded the protection that a player giving the signal has.

This is a play where the covering official has to help out. The R player may not have seen the FC signal and doesn't know the ball cant' be returned and K may not have seen it either and thinks R is fair game. Once you are sure the catch has been completed (watch for the muff), blow the whistle and stop the play before anything bad happens. Don't get bent out of shape if R starts to run, just keep on the whistle until he and everyone else stops.