In the past, studies have shown that impact forces are higher with more cushioning in the shoe. Conversely, unshod runners were shown to have the lowest impact forces on the foot.

A new study suggests that we have interpreted this data incorrectly. These studies suggest that the loading is the same, but that the characteristics of the loading are spread into two distinct impulses with more cushioning. In unshod runners the impulses "run together" because the initial impulse is delayed by your bodies ability to adjust to a variety of shoes and cushioning. This lends weight to the argument that your should Run in a variety of shoes.

References:

New Research on the Science of Barefoot Running
...we’re wired to automatically adjust our biomechanics to keep the overall loading rate roughly the same... runners adjusted the angle of their foot strike to control how long that [lower leg] impact took. When barefoot, they landed on their forefoot, which prolongs and softens the landing, with the calf muscles and Achilles acting as a shock absorber. In the thick-soled trainer, the presence of cushioning allowed them to slam down directly on their heel, which led to a sharper J1 curve without changing the overall loading rate.

What’s key here is the timing of that impact peak. If the initial peak is delayed long enough, it effectively disappears into the main peak [of the overall loading on the leg]...you reduce one of the forces but increase the other, and end up with a similar total force.