Currently, yes. The article is positing that once Apple has the infrastructure in place for end-to-end transactions, removing the VISA/MC puzzle piece will be easy. Ultimately, you'd put money into an Apple account and spent it on your iPhone.
I don't think you are very familiar with how the payments industry works. Credit cards offer much more than a means to pay. Apple will need to double their headcount to compete with Visa. Or do you think that this is a feasible scenario?