That Southwest airlines jet where half the people weren't onboard? That just got converted into (200 seats * 200lbs lardass Americans) = 40,000 lbs. of roses, prawns and couriered legal documents.
The fact that you're not farting into a foam cushion doesn't matter to the operator or the environment. It just means less cattle are in the boxcar.
Here's how the problem is presented: more people want to fly, but they like fresh flowers, fresh food and, more than this, fast package delivery. Your girlfriend who swears she's helping the environment by insisting on organically-farmed New Zealand lamb? Your dad who overnights parts for his biodiesel conversion? Your mom who wants domestic roses fertilized with only the freshest of cow shit? Yeah, they're dumping hydrocarbons into the atmosphere with every dollar spent.
Fuel on a 747-200 burns at ~23,700 lbs./hr. during cruise flight, more during taxi operations.
Pounds. Flight. More during taxi. You know what taxi operations are, right? Where you're waiting on the tarmac? Happens a lot, doesn't it?
Cargo gets consolidated per air carrier for environmental and operational cost purposes. It just does.
The reason why more empty seats equate to less environmental damage (at least in my mind) is that you're staying at home instead of using the extra energy to get to the airport. Those planes will keep doing what they're doing, no matter what, unless you refine your behavior.
Worried about carbon? Worried about environmental impact? Buy local only. Cut down on time in cars/taxis. Ride a motorcycle. Eat less. Drink tap water instead of anything else. Grow your own food.
Otherwise, do what I do, stick your fingers in your ears, say "lalalalala" and enjoy living in the first world.