Maybe a bit more background (based on my reading of the German Wikipedia article):
As the others have said, this is to do with how VAT is calculated for the seller. Specifically it is applied to goods that the seller itself bought without VAT being 'declared' (e.g. when he bought the item from a private individual). In that case, the seller is only VAT liable for the difference between the price he paid for the item when he bought it and the price he is going to sell it for (that's why the rule is also called the 'difference rule'). The article gives the example of a used car salesperson. This reduces the VAT liability to the seller thereby effectively increasing his margin (the amount of money he's made from the sale). The downside for the buyer is that he can't reclaim this VAT amount. However, if you (as buyer) don't fall into this category anyway (i.e. buy as a private individual) this is the cheaper option for you as well. If you buy as someone who can and wants to reclaim VAT, you would be better off using a different rule (paragraph 12).
There's more to it, but that's the gist (I think).