There are many reasons for this and as mentioned one is employee theft. If you've ever owned or operated a retail type business you would know there is much involved in reconciling the cash sales vs. what the register shows.

Also important to note that the items mentioned are discretionary and entertainment. As such it's not unfair at all to have to pay more if you want to pay in a way that the business requests. There is no obligation for a business to support payment methods that require them to increase costs (in theory) for all customers to cover the loss of dealing in cash. (Also removes potential issues somewhat with money laundering).