If I understand what you want and if the rows have a multiple of three elements, this should work for you:
X = xor(xor(M(:,1:3:end-2),M(:,2:3:end-1)),M(:,3:3:end));
If this is not what you want, you should clarify that phrase "every three bits together" so that it is clearly understood. As it stands, it is easily misunderstood. It should be simple to make it clear what you mean if you carefully construct a good, meaningful example.
