You can use combnk() to create the permuted column indices for each row of your matrix and then replace those values by 0.
% Generate some data
z = ones(6,4); % your original matrix
nzeros = 2; % number of zeros to add to each row
Solution:
permIdx = combnk(1:size(z,2), nzeros); %permutation index
linIdx = sub2ind(size(z),repmat(1:size(permIdx),nzeros,1).',sortrows(permIdx));
z(linIdx) = 0;
