It is at the very least unusual, but there is a reason for it in this case. The idea is to encourage a bank to lend its money elsewhere – for example, to businesses. That is one effect of negative rates. And there is a second effect – aimed at investors in the financial markets.
Better access to non-bank financing, notably equity capital, improves firms’ financial structure, supports innovation and makes them more creditworthy, thus safeguarding banks’ balance sheets and avoiding vicious firm-bank loops. This is not to deny that the CMU can put pressure on banks.