First, I have to say I am a huge fan of Vibram Five Fingers shoes. I believe they are an excellent product! I personally own two pair of KSOs and plan on buying the new Treks when they become available. I highly recommend the shoe to anyone interested in going the minimalist route.
Having said that, I do believe there is a time and a place for ANY minimalist shoe. If you are interested in learning to run barefoot or make a switch to a minimalist shoe, start barefoot. If you start barefoot, you will learn proper technique and form in a short time. Encasing your feet in any sort of shoe will simply inhibit that process. If you have no intention on running barefoot and are only interested in moving to a minimalist shoe, that transition will be greatly facilitated by learning barefoot form first. Use the minimalist shoes once you learn the form.
To learn good form, it is critical that your brain receive accurate sensory feedback from the rest of your body. This is especially true of your feet. The soles of your feet will tell you if you are overstriding, running too fast, or creating too much friction. If you cover your feet, even with a minimalist shoe such as the Vibrams, you will short-circuit that neural pathway. Too many people seem to be tackling barefoot or minimalist running too aggressively, which leads to injury. Resist that temptation!