The volunteers that organise audaxes choose how they want payment. Most now are happy with paypal (since AUK put some time into sorting out an integrated system for it), but some organisers are not particularly computer literate, or don't trust their bank details to computers, and I would prefer them to offer events with cheque entry over focing every organiser to take online payments and losing good organisers such as Dave Hudson.
If you really can't handle cheques, ask the organiser if you can pay on the day.