It's all about acceptable risk. Each confirmation adds additional security to your transaction. 1 confirmation is easier to reverse than 6 confirmations, and 6 confirmations are easier to reverse than 100 confirmations. 6 is simply taken as a commonly used "trade-off" between time and security.

Many exchanges and services will accept a bitcoin deposit after 1 to 3 confirmations below a certain limit. There is a slightly higher risk of reversal, but they can tolerate that for lower sums of money. But for higher sums of money then they want more confirmations. If I was selling some second computer parts, then 1 or 2 confirmations would be fine. If I was selling a car, then I'd be waiting for 4-6. If I was selling a house, I might want even more than 6. The longer you are prepared to wait, the more security you achieve.