Although security measures are never foolproof, the Apple Pay system is safer than many current pay methods.
For one thing, a substitute account number is assigned when you set up Apple Pay. Merchants get that instead of your real card number. In addition, a verification code is created for each transaction, based in part on unique keys on the phone. Even if hackers get that substitute number, they wouldn't be able to generate the verification code without having possession of your phone, so fraudulent transactions would be declined.
Other services are starting to use one-time verification codes, too, but not all of them use the substitute account number. By using that substitute, a credit card issuer could cancel the number just for the phone, should you lose it. You wouldn't need to replace the entire card.
Apple says it knows nothing about your transactions, which are handled directly by the credit card processors.
