First, we have to decide what kind of VTOL we are going to use- tiltrotor like Augusta WestlandAW609, compound helicopters like Eurocopter X3 or using jets like the F-35.
For commercial operations, the first two are not very suitable as they lack the speed and carrying capacity. At best, they can act as costly and complicated propeller aircraft, which are not the main type in use. So, lets consider the jet aircraft.
Actually, there was a vertical takeoff jet transport, the Dornier Do 31. It is instructive to consider what happened in this case. It never got past the prototype stage.
"Dornier Do 31 in 1968" by Ralf Manteufel - http://www.airliners.net/photo/Germany---Air/Dornier-Do-31E/1265410/L/. Licensed under GFDL 1.2 via Commons.
For takeoff, the VTOL aircraft has to produce quite a large amount of thrust- Do 31 used a grand total of 10 engines, including 8 exclusively for vertical takeoff. The engines produced a total thrust in excess of 290kN for lifting the 27 ton aircraft (not at its MTOW). In contrast, the 50 ton Boeing 737-100 had engines that produced a sum total of 128 kN.
Even military VTOL aircraft like the Harrier and F-35 were not able to take off vertically at their full load. In fact, Harrier was rarely used operationally in VTOL mode. In most of the cases, it was operated in a rolling takeoff.
VTOL mechanisms are complicated. You've to either swivel the engine thrust (like F-35) or use separate engine(s) (like Do 31) for vertical takeoff. In either case, you're having dead weight. This increases the fuel and structure required (for support), which leads to further weight and fuel requiremetn and so on.
The fuel consumption for VTOL would be enormous. The economics is against the operation of VTOL aircraft.
More complicated the mechanism is, more chances of failure. Not a good thing in commercial operations.
As for compound helicopter, the Fairey Rotodyne was designed with commercial transport in mind; however, noise considerations (among others) killed the project. Of course, if a large rotor is used, the drag will be prohibitive at high speed.
Image from jefflewis.net
AW 609 was the first tilt rotor to be developed with commercial operations in mind. However, with the fatal crash of second prototype, it remains to be seen if it will succeed.