No amount of cushioning in a shoe can adequately protect our knees, backs, etc. from the pounding of heel strike running. Unfortunately, the way shoes have been designed since the 70's (Nike) with ever changing styles of cushioning in the heel, almost all of us are "heel strike" runners. The idea behind barefoot running is to gradually change the way you stride. If you take your shoes off and stride leading with your heel, it's gonna hurt! It is true that there are runners out there running with minimalist shoes or barefoot that are able to avoid injury. This is not something that can be accomplished overnight. These folks have gradually adapted their running mechanics (short distances, soft surfaces, etc) to become capable of running "barefoot". They take shorter strides, have more forward lean, and land more on the ball of their foot which does reduce impact with each stride.
There are benefits to re training yourselft to be able to run barefoot and yes, the shoe companies are also marketing and capitalizing on the craze. Just taking off your shoes or buying a pair of Nike "Frees" without focusing on mechanics and building up VERY gradually, will result in injury to 99% of the runners out there.
If you are going to try it, I would suggest working into it very slowly (neutral running shoe short distances). It also feels good to take your shoes off after a long run and walk barefoot as you cool down. If the shoes come off, run on soft surfaces like grass or sand. Continue researching the pros/cons and take it slooooow, all the while focusing on changing your stride. With all this said, there are some body types/biomechanic combinations that will never allow for injury free, barefoot running
Did I mention, TAKE IT SLOOOOW?