As stronger fuel demand and Egyptian unrest pushed crude oil prices over $100 barrel this week, the transportation industry renewed the debate over how to stabilize fuel costs by the increased use of electric vehicles and alternative fuels. But unfortunately these businesses — from airlines like Delta (NYSE: DAL) to freight companies like FedEx (NYSE: FDX) to businesses like Waste Management (NYSE: WM) that have large truck vehicle fleets — don’t really have any alternative in the short term.

Although many in government and the transport sector agree that migration to cleaner energy sources will be an operational necessity by the middle of this century, there are few viable alternatives to fossil fuels available today. And the promising — but expensive — solutions on the horizon are unlikely to have the needed impact for decades.

“Every 24 hours our aircraft fly 500,000 miles, and our couriers travel 2.5 million miles. We accomplish this with 670 aircraft and 70,000 motorized vehicles worldwide — nearly every single one of which is fueled by oil, the lifeblood of today’s mobile, global economy,” FedEx (NYSE: FDX) CEO Frederick W. Smith wrote in a Fortune column this week. “We cannot continue down this path.”

What path is that, Fred? The business of shipping packages? FedEx and its top competitor United Parcel Service (NYSE: UPS) clearly don’t want to cut back on the miles they travel or the customers they serve — so of course it’s in their Smith’s best interest to propose that someone (Uncle Sam) help keep margins fat.

The solution, Smith believes, is for the federal government to throw its weight behind electric cars and trucks. He makes a valid point that promoting and subsidizing electric cars and trucks can have a positive impact on reducing oil consumption, boosting fuel efficiency and cutting costs. But any real solution for slashing the transport sector’s reliance on finicky fossil fuels must address these issues, too:

Global Demand for Hybrid and Battery Electric Vehicles May Be Over-Hyped. In an October 2010 study of future demand for hybrid and battery electric vehicles, J.D. Power and Associates said green cars and trucks would account for only 7.3% of global sales in 2020. Why? Consumers don’t like their look, power and performance — and despite flashy ad campaigns, they worry about reliability, range and the time it takes to recharge batteries. And while the Chevy Volt won 2011 Car of the Year honors with its 93 mpg electric rating, General Motors (NYSE: GM) delivered only 321 of the vehicles last month. By contrast, it delivered 28,172 Silverado C/K pickups (which get about 20 mpg) — up 23.7% from January 2010.

‘Green’ Regulations and Subsidies Can Cost Jobs as Well as Create Them: In his State of the Union address last month, President Obama vowed to use regulatory and tax incentives to break U.S. dependence on oil by boosting biofuel and electric vehicle development. Long term, investing in green technology and development makes sense because it’s the right thing to do environmentally and economically. But according to Dr. Jonathan Lesser, an economist with expertise in the energy industry, using regulations and taxes to jump-start renewable energy can cause “reduced economic growth and fewer jobs overall” by placing restrictions and penalties on the bigger, established businesses that use fossil fuels. Is that a reason not to go green? No. But it may be a reason not to go green immediately while the recovery is fragile.

Biofuels Offer Promise For Airlines, But Replacing Oil-based Fuel Will Take Time. Advances in electric vehicle technology won’t help cut airline fuel costs. By Mr. Smith’s own admission, that’s 500,000 jet miles a day his company will not be offsetting even if Uncle Sam subsidizes electric vehicles. Biojet fuel – which is made from agricultural residue, algae, landfill waste and other sources – can help. But even if biojet fuels can be developed quickly and economically, they will be subject to extended tests before they can be integrated into air carrier operations since they will impact flight safety and aircraft lifetime. Boeing (NYSE: BA), Air China Ltd. and PetroChina plan to conduct flight tests of a nut-based biojet fuel on one of the airline’s 747s later this year — a good start toward achieving the long-term goal, but no relief in the near term.

Bottom Line: When it comes to kicking the habit of pricey foreign oil, there are no quick fixes. Transportation companies are well served to seek out cheaper fuel sources as a means of beefing up their bottom lines. But deficit-busting government subsidies won’t pay dividends for decades and are likely to stall economic growth and slash jobs in the near term. And a relapse into recession would hurt everyone — including transportation companies.

Still, odds are that innovation and investment in clean energy eventually will reshape the transport industry in the 21st century as dramatically as airplanes did in the 20th, although the times and methods are as hard to predict today as they were back then.

“I confess that in 1901, I said to my brother Orville that man would not fly for 50 years,” Wilbur Wright told the Aero Club of France in 1908. “Two years later we ourselves made flights. This demonstration of my impotence as a prophet gave me such a shock that ever since, I have distrusted myself and avoided all predictions.”

As of this writing, Susan J. Aluise did not own an interest in any of the stocks mentioned here.