Is my money safe at FNB?

So I just went to FNB to complain about a glitch in their system, the response I got was "We can do nothing on our side, it's the merchant".

To put things into context: I disturbingly discovered yesterday that when my cheque card is swiped, it does not ask for a pin number. I do not have the 'tap' enabled card because I feel it is a security risk... But apparently my "chip and pin protected card" is in fact not entirely pin protected.

The assistant at FNB tried to convince me that the error lies on the merchant side. The merchant I visited was Food *****s Market in Somerset west. Apparently on the merhant's system they are able to by-pass your pin number. Why do I then have a pin number on my card if someone on the merchant side is able to by pass it WITHOUT my permission AND WITHOUT knowing my pin???

I am extremely dissatisfied that my query and complaint was not taken seriously at FNB, and that it was placed in a report "to be taken further".