I'm not sure what there is to explain. As documented, col tells you where each element corresponding element of C is found in S. If the element of C is found in more than one position, you'll get the first one of these.
The code is also flawed and will error if any element of C is not found at all in S. The safe version of the code would be:
S = [1 3 0 2 0 0];
C = [0 2 4]; %note that the original code would error because 4 is not present is S
[found, where] = ismember(C, S);
S(where(found)) = [] %this will not error
