The British Olympic Association said in a statement on Friday its four-member Olympic qualification standards panel had agreed to back east Londoner Lutalo Muhammad over European champion Cook in the -80kg division.
The decision triggered accusations that the selection was politically motivated and punishment for Cook leaving British Taekwondo's performance programme to train separately.
In an interview with Wednesday's Daily Telegraph, Cook said he merited a place in the team and that his "nightmare ordeal" did not bode well for the future of the sport in Britain.
"This has never been a personal battle between Lutalo Muhammad and myself," he said. "The fight is me versus GB Taekwondo, which is denying my childhood dream of Olympic gold - a dream I believe I had earned through my performances.
"My results are vastly superior to Lutalo's. The quality of players I have faced is far higher and I have won nine of my last 12 tournaments."
Cook added: "I will never believe or be convinced that my non-selection for my home Olympics was not politically motivated.
"When my non-selection was announced I had the right to challenge its process via a quasi-legal body called Sports Resolution.
"Their findings were very conclusive but we are not allowed to discuss them or release them. Why have I not been selected? Simple. Because I left the British Taekwondo system last year."
Cook went on to explain the reasons behind his decision to drop out of the system.
"My form was not good enough while in the academy," he said. "I lost three matches in a row, including at the 2011 world championships. Seven weeks prior to the tournament the GB academy pulled my coach, Professor Moon.
"I had previously been given assurances he would be my coach until London 2012.
"Instead I was forced to work with a coach, Steven Jennings, with whom I had no relationship and who already had responsibility for three other athletes, including his wife who would fight on the same day as me.
"It was crazy."
Cook said he feared for the future of taekwondo in Britain and was worried that he might never have another chance to fight for an Olympic gold medal.
"It saddens me this whole debacle has happened, it brings our sport into the headlines for the wrong reasons," he added.
"I have not been treated fairly or respectfully in this whole process. This may actually be my last Olympic chance - I hope not.
"The message to future Olympians is: 'It is not about performance. It is about the system protecting itself'."