They couldn't take off from the gates, as they would still need quite a bit of clearance from the jets pointing down at the ground. Also, my understanding is that pure VTOL cannot accomodate large payloads, so that may be a limiting factor for commercial airliners. I would assume that even STOL would face payload limitations compared to conventional aircraft. Also, I would guess that fuel consumption would be an issue.
If only we could get those anti-gravity devices working, all our problems would be solved...
EDIT: googled and little and found this. REsponse seems to make sense.
http://www.answerbag.com/q_view/43931
Another big issue for VTOL (vertical take off and landing) as opposed to STOVL (Short take off, vertical landing), is engine thrust v's weight.
In order to take off vertically you must have more combined engine thrust than weight.
Harriers cannot take off vertically when fully loaded - their weight exceeds the thrust of their engine. Instead, they take a short run-up and then used vetical thrust to assist lift-off, or they use a short runway with a ramp at the end to launch into the air.
With most commercial aircraft weighing in at over 100 tonnes fully laden, you would need very powerful engines to lift off vertically.
As an example, the 747 weighs several hundred tonnes, but the engines they've had up until recently only put out about 25 tonnes of thrust each (about 54,000 pounds of thrust). It's plenty for horizontal propulsion, but nowhere near enough for vertical.
The most powerful jet engine I'm aware of at the moment are the Rolls Royce Trent turbofans. The Trent 900 series were somewhere up around 100,000 pounds of thrust (about 45,000kg). I believe these engines will be used to power the Airbus A380.
Another big issue would be structural design. Only one V/STOL aircraft that I know of has its propulsion outside its body - the V-22 Osprey. Most V/STOL (Vertical or short take off and landing) aircraft have their engines and propulsion nozzles in the body of the aircraft. An aircraft with pod mounted jet engines, as most commercial aircraft are, would put enormous strain on the structure of the wings if they had vertical thrust. You would also need to add maneuvring jets for the nose and tail and wingtips to give directional control during vertical thrust operation.