We now use EFT and Bpay rather than cheques. From the experience of our strata, I can say NO! It is not usual. Nor should you accept it. Our strata was charged $1 for every cheque we drew, we then changed to doing all our transactions on line and we now get no charges.
As I understand the current state of financial deregulation such fees and charges are up to each bank or financial institution. If the fee is charged because you use a credit card and the fee is charged by the card company that is a different argument.
Look around and negotiate with your financial institution. We use a Building Society. All the executive has access to the account and each BPay or EFT has to be authorised electronically by two members of the executive. In terms of transparency and accountablity moving to electronic online transactions has been a real boon to our strata!