Apple could have done what PayPal does but they chose not to.
There are many reasons for this, but perhaps the most significant one is that they do not have to, or want to, have all of the credit card numbers in a database so that they can charge them for the merchant - the way that PayPal does.
Apple is implementing a very new part of the credit card processing system - EMV Tokenization - which is one of the most secure ways to process credit cards at retail point of sale - where most of the recent attacks have been happening.
In order for a card to be used with EMV Tokenization, the bank that issued the card has to support the new standard as well - and has to agree to work with the tokenization provider (in this case, Apple). Not all banks are ready to support EMV Tokenization and not all of those that do support it are willing to work with Apple.
In the long run, virtually every bank will likely get onboard with EMV Tokenization in general (and quite likely with Apple in particular).
EMV Tokenization reduces the chance of fraud because the token is unique for each transaction. Apple's implementation - tied to Touch ID and the Secure Element in the A8 child - is more secure even than that because the generation of the token for a given transaction is tightly tied to the owner of that phone (or next year - that specific watch).
These two things together will virtually eliminate the usefulness of mass credit card data breaches. THAT is why the banks are willing to give apple a small piece of their cut for transactions that get processed through Apple Pay... because even giving Apple that money they stand to SAVE a whole lot of money in reduced fraud.
Apple is the logical "launch partner" for such an initiative because very quickly there will be tens of millions of iPhone 6's out in the wild that can take advantage of the system. But there's no reason to think that other phone manufacturers can't/won't build the same sort of capabilities into their phones/smart watches... even without the TouchID part, EMV Tokenization will still reduce fraud greatly.