The 21-year-old was world number one in the under-80kg category but Lutalo Mohammad was instead selected by British Taekwondo leading to a drawn-out process which was eventually ratified by the British Olympic Association.
Mohammad won the bronze medal at London 2012 in what was a successful Games for taekwondo as Jade Jones won gold in the women's 57kg category while Martin Stamper reached the semi-finals.
However, it was Cook who dominated the column inches in the run-up to the Games and now he has decided to compete for the Isle of Man in all events bar the Olympics.
Manx athletes compete under the GB flag at the Olympics but, according to Cook, the World Taekwondo Federation (WTF) may introduce a route to the Games based on rankings rather than discretionary selection which saw him miss out this year.
Cook told Sky Sports News: "I was reigning European champion, world number one - I am never going to work with those people (British Taekwondo) again.
"They have made their minds up with what they have done to me and I've made my mind up.
"I think I am quite lucky at the moment, the WTF are looking to organise new competitions, such as a grand prix, which they have said will open up a different path to the Olympics based on world rankings so all I have got to do is go and win the World Championships, the European Championships and make sure I am top ranked in the world and I can get there off my own back which we didn't have in the past."
Of his disappointment on having to look on rather than participate in the summer, Cook added: "I am extremely jealous obviously, I wish that was me.
"She (Jade Jones) did fantastic and so did Lutalo and so did Martin Stamper.
"I just wish I could have been on that team, I felt I deserved to be on that team.
"I've got to find some peace and I've to go move forward and this Isle of Man [opportunity] has come up and I can't wait to be hopefully world champion next year."