For every fraudulent credit card transaction that is caused by employee theft there are millions that come from hacked credit card numbers. Actually it is almost a statistically certainty that at some time in the recent past your credit card and debit card numbers have been stolen and were available for purchase and use by bad guys.
These bad actors normally make small charges across thousands of cards, making the pursuit and prosecution of any one charge impossible.
The odds that the OPs case was actually an employee is very, very low. Any such activity would quickly be discovered and the employee arrested. Much more likely the card information was either hacked or stolen by someone looking over the OPs shoulder.
And yes, Credit Cards are the safest way to make any transaction. Debit card transactions are now generally guaranteed by your financial institution, but it isn't as clear cut as the protection a true Credit Card gives you. With a credit card, all you will be out, should your card be compromised, is time and effort to get it resolved. Once your cash is stolen, it is gone. And in the event you ever need to prove you actually paid for a purchase, a credit card transaction doesn't get ruined when you wash it like a receipt for cash does. For security, Credit Cards get two thumbs up with a double snap!