Why was the Concorde retired in 2003 despite having a good operational history barring the 2000 crash?

TLDR

It wasn't economical anymore. (or so it was claimed)

The long Version

Research and Development[1]

The Concorde was a watershed in terms of complexity and scale in aircraft design  when work began on its design in 1956. Controllable supersonic flight was then a relatively new area and the understanding of the science behind the effects of compressibility and its effect on aircraft handling near the sound barrier was still in its infancy.
Design and development of a supersonic transport (SST) was a source of national pride then and the British interest in entry into the European Common Market forced them to sign a deal with the French government and arranged a joint venture between the British Aircraft Corporation and the French airplane manufacturer, Sud Aviation (later Aerospatiale) in a joint venture. Reflecting the latent nationalism on both sides the deal was signed on the basis of a national treaty rather than as a deal between two corporate entities.
Two separate aircraft, the BAC 221 and the HP 115 were built to explore the handling of large delta-winged aircraft at high and low speed ends of the flight envelope respectively and while both the British and French teams initially agreed on the design, costs and times were protracted with the projected unit cost more than tripling by the time the R&D work was over. 

HP. 115

Fuel Costs and Sound pollution concerns[1]

The Concorde design started in the era of cheap aviation fuel and as a result fuel economy was never deemed to be a constraint. The Oil crisis of the 1970 s made it extremely expensive to operate, and forced a large number of would-be operators to rethink their options.
Ironically enough, the the raison d'atre  for Concorde's existence -its supersonic ability also turned out to be the biggest barrier to its widespread use. Tests over Oklahoma City in the US made it clear that sonic booms from SSTs were quite capable of reaching the earth and this ushered in a new lobby of environmental concerns that pressurized governments the world over to ban Concorde's flights over land. Coupled with the oil crisis, this reduced the number of potential customers from 16 to 4 and finally 2. British Airways and Air France became the launch and only customers of the aircraft, restricting them on transatlantic crossings where supersonic flight was permitted, with both governments taking a cut of the profits.

Heyday of Luxury Aviation

Age and Safety concerns [2],[3]

At the beginning of the 21st century the Concorde had become undeniably dated. As it had had no competition in its unique market niche, developmental pressures that had forced more conventional airlines to economize and introduce computerized flight systems had passed it by. By 2000 its cockpit still had analogue instruments and it was the only aircraft in the BA fleet that still retained the position of a flight engineer in the cockpit.

Then came the much publicized crash of  Flight 4760 in France where pieces of a ruptured tyre damaged a wing fuel tank during take-off leading to a subsequent fire and crash of the Concorde involved . While the accident itself was a result of an inherent danger in aviation - that of foreign object damage (FOD) - rather than the design flaw of the aircraft, it forced the shut down of all flights over a year until safety measures put in place and further extensive testing was conducted.
The first flight after the crash was on September 11th 2001, landing soon after the attacks on the WTC and whatever hope the Concorde might have had of making a come back was quickly quashed by the air travel slump that followed. The final nail in the coffin was Airbus's (inheritor of the Aerspatiale's mantle) refusal to support the maintenance and manufacture of spare parts.

It was all down to Cost: The Airlines were not making back the money spent on the safety modifications and other upgrades, with some other big costs coming up (tens of millions, before any life extension programme), BA needed to write off £84M now rather than £150M in 3 or 4 years. Air France wrote off a large sum  too.

In April 2003, both airlines announced that they were going to retire the Concorde later that year. Richard Branson bid heavily for purchasing the fleet stating that Virgin Atlantic would continue to operate the aircraft for many years to come, but nothing came of it. While it soon became apparent that the airlines could still operate Concorde economically in the subsonic mode, the security implications in the post 9/11 world coupled by a lack of maintenance and its age finally forced the graceful yet aged giant from the skies.

Concorde on it's final flight

EDIT

Sources

[1]Concorde : Story of a Supersonic Pioneer - Kenneth Owen

[2]The Crash of the Concorde - Ann Byers

[3] The Definitive Concorde Aircraft Site on the Internet

Thanks for the  A2A!

On 10 April 2003, Air France and British Airways simultaneously  announced that they would retire Concorde later that year. They cited  low passenger numbers following the 25 July 2000 crash, the slump in air  travel following the 11 September attacks and rising maintenance costs.  Although Concorde was a technological marvel when introduced into  service in the 1970s, 30 years later its cockpit, cluttered with  analogue controls and dials, looked dated, as there had been little  commercial pressure or reason to upgrade Concorde due to a lack of  competing aircraft, unlike other airliners of the same vintage, for  example the Boeing 747. By its retirement, it was the last aircraft in  British Airways' fleet that still had a flight engineer; other aircraft,  such as the modernised 747-400, had eliminated that role.

1. Relatively less profitable than the other aircrafts in BA and Air France's fleet. When Concorde was suspended for a short time after the accident in 2000, both the airlines realised that their passengers remained loyal to the airline brands and flew First Class in their subsonic aircrafts instead.
2. High Operational Cost - The maintenance cost and fuel costs per passenger where too high considering the limit in the payload the aircraft could carry.
3. Environmental issues - Concorde could do supersonic only on international waters, which limited its reach and network to flying supersonic above other continents (Not to forget its very own 'Europe')
4. No keen interest by the British and the French Government to upgrade the aircraft or its technology. Concorde was the only aircraft in 2000 which housed a Flight Engineer - a position eliminated by all commercial aircrafts due to sophistication of the Cockpit instruments. While the entire world had moved into digital glass cockpits, Concorde still flew with the analog instruments and gauges in the cockpit.