Do the math. If we're generous and say that Lightning cables/adapters cost $3 to manufacture, and they retail for an average of $30, that's $27 in profit for Apple and their retail partners.
Now imagine only the opening weekend iPhone 5 buyers, all 5 million of them. They on average have two accessories/locations that need adapters/cables. 5 million x $27 = $135 million in profits on the opening weekend alone. Profits that wouldn't exist if they went with the smaller, more commonplace microUSB.
Of course, that's a low estimate. Mass produced accessory cables typically cost around 25 cents or less to manufacture (microUSB, Apple 30-pin). I don't really think the authentication circuitry inside the Lightning cable costs $2.75 to produce, but I'm giving Apple the benefit of the doubt since it's a brand new connector for them.