You are correct about the origin of the term "Black Friday," but it is actually no longer the case. Most companies are designed to lose money on Black Friday. The extreme sales are a way of attracting attention and building a customer base. Most stores will already be in the black before the day after thanksgiving, will take a hit on that day, and will recover in the weeks to come with "real" holiday shopping.
When Circuit City sells a laptop for $300, they aren't making money, unless they add a $150 protection plan, a laptop case, and anti-virus software onto it. That goes for more than half of the laptops, not only Black Friday ones. They have a negative margin on mainly Acer, HP, and Compaqs, but also some Toshibas.