First, it's the mass (and really the distribution of the mass) that matters; not the radius (if you do the full calculations with moment of inertia, etc, you'll see that the radius of the wheel drops out of the equations). Now, bigger wheels are generally heavier, so it's almost true that bigger wheels are slower.

Second, the bike isn't just wheels. When you accelerate the bike, you've got to get you and the whole bike moving. And you are much heavier than the wheels (even if you're tiny).

As far as that article goes, the author says many things in the article that are wrong (e.g., smaller wheels are easier to accelerate, bigger wheels have bigger contact patch). The author's degree is in psychology, not physics or engineering, but that's not really a good excuse.

You'll also hear exactly this in a lot of bike shops: Dude, spend money, get the lighter wheels, you'll accelerate faster. I don't think they're lying just to sell you wheels. But they're still wrong. (Aerodynamic wheels, on the other hand, will help you go faster.)