The Prius wasn't free. It cost him about 24k sticker price (according to him).
Just because it saved him from wasting money like he was doesn't make it free.
To illustrate my point, let's look at an example. Let's say I take up smoking, then quit. And I go "I saved $5/day in packs of smokes! After a year, that's about $2,000, or 4 free iPads - quitting smoking got me 4 free iPads!"
..no.
Quitting smoking got me money back that I was wasting. But it didn't make the item I bought with that money free.
He was wasting money having two vehicles. By switching to one, he saved a bunch of money. The fact that he replowed that money into a Prius doesn't make the Prius itself free, just like by plowing smoking money into iPads it doesn't make the iPads free.
Almost all his savings had to do with switching to one car (less miles driven, less insurance paid, less car payments, etc.). Overall, I agree with you though, that it is an interesting look at the financial costs of car use. The author's conclusion of a "free" car, however, is just ridiculous sensationalism to catch eyeballs.