Samsung’s newest flagship device Galaxy S6 comes with a breathrough mobile payment system that basically works with all credit/debit card payment terminals, no need for special NFC equipped machines or such, just take your S6 near to any credit card terminal and you’re done. Payment will be made.
However, if you’re planning on rooting your Galaxy S6 with a method that trips the Knox counter, like the CF-Auto-Root, then it’s very unlikely that you’ll be able to use Samsung Pay on your Galaxy S6.
Rooting your Galaxy S6 with CF-Auto-Root will install a custom binary on your device, which trips the Knox counter, and is also the main reason for not being able to use Samsung Pay on a rooted Galaxy S6.
But we aren’t sure yet if an untripped KNOX will be a requirement for Samsung Pay or just Samsung binary (stock firmware) will do to get Samsung Pay to work again, once the Knox flag is tripped. This we’ll be verifying as soon as Samsung Pay is made available.
Chainfire, who develops and maintains the CF Auto Root package has the following to say regarding Samsung Pay and rooted Galaxy S6:
Before actually rooting though, consider that KNOX will likely be tripped, and there’s a good chance untripped KNOX will be required for phone based payments.
We suggest you to not root your Galaxy S6 or trip the Knox counter until this is cleared — that is, if you care about Samsung Pay.