Who said most people still use the unpaid version?
Tons of people (from forums etc) use v3, which means they paid for v2 (or pirated it). I have paid for v2 and use v3 myself.
He also hired an extra guy during v2 development, which means he made enough money to have that. And in general, it's a hugely succesful project with Windows and OS X users.
If John saw that the unpaid version was an issue, he'd just cancel it.