In your case, [1,1;1,1] == zeros(2) creates a 2x2 logical array. If the argument of an IF command is an array, Matlab converts it as this automatically to:
if all(Condition(:)) && ~isempty(Condition)
If you want to check for a "zero-matrix", prefer to do this explicitly:
if all(M(:)) && ismatrix(M)
This is easier to understand than using the automagic convertion.
if isequal(X, zeros(2,2))
is valid, this wastes time by creating the temporary zero matrix. If you want to check, if all elements are zeros, prefer only to check if all elements are zeros. :-)