That's pretty much the idea. Those with poor foot design couldn't outrun the carnivores, didn't survive, didn't pass on their genes. Only those with the best foot design survived and passed on their genes, resulting in our current design after millions of years. The current design could use some improvement though. The ankle is too fragile and the soles are too susceptible to punctures and cuts.
The problem I described is well known within theoretical evolutionary literature. The basic idea is that if mutations find a method for some task, natural selection will then refine the method to whatever is optimal, but only in gradualistic steps because the odds of multiple coordinated mutations occuring in a single organism is too low. So if a poor initial design is chosen you end up with an optimized poor design, even if much better designs are available via different evolutionary pathways. We should expect sub-optimal designs to greatly outweigh the best solutions in nature if they were chosen by chance factors due to the variety of potential solutions to any given task.
The current design could use some improvement though. The ankle is too fragile and the soles are too susceptible to punctures and cuts.
If you read the article, you'll note that toughening the soles would be contradictory to some of the advantages to running barefoot in the first place. Soles are already pretty tough, such that hardening them further would not make a huge difference (i.e., shards of glass have not been a hazard for most of human experience, for example), and the extra weight would be a constant drag. Better to let us tool users design hardened boots for those occasions when we need them.
As far as the ankle, it's a similar problem of balancing strength with flexibility and mass. Let's put it this way: people who believe in evolution are forever claiming that various body parts are badly designed - and then failing to specify an improved design. Where are the Evolutionary Science clinics with crowds of people entering them to get improved ankles, improved knees, improved eyes, and so on? There aren't any, beause the claims of poor design are poorly conceived (as repetively demonstrated in critical reviews on the subject).