As I recall England were leading 2-1 when Sir Alf made 2 substitutions (Norman Hunter for Martin Peters and Colin for Booby Charlton). West Germany had just scored with that shot by Beckenbauer that went under Bonetti. Some argue the substitutions signalled that England were happy to try and see out the game and that gave WG the additional momentum. Others that taking off a 32yo Charlton in the blazing heat of Mexico to save him for the semi final and replacing him with the fittest, strongest squad member in Bell was a sensible move. Colin set up a great chance for Hurst that missed by inches and was brought down for a certain penalty by Beckenbauer that wasn't given. Remember that the referee was from Argentina. Four years earlier Ramsey had called the Argentines "animals" in the QF at Wembley - something they had felt insulted by. He also said that Mexico was not a safe country from a food and hygiene standpoint so that had offended the authorities of the host country. Everyone was rooting against England so it's no surprising decisions went against them.
WG - a great team - piled the pressure on and equalized through that freak backward header by Seeler, with Bonetti caught in no mans land as it sailed over him to take the game into extra time. England, under Ramsey, relied heavily on their full backs (Newton and Cooper) to get forward and overlap to support attacks but in the heat and humidity of Mexico were vulnerable defensively and as extra time wore on WG exploited this and substitute winger Grabowski set up the winner by beating Cooper and crossing for the great predator Gerd Mueller to smash in the winner.
Of course the media had to look for someone to blame and sacrificing the legendary Booby Charlton (the darling of '66) was an easy target with which to beat Ramsey with. Charlton had an average World Cup in 1970, he was clearly past his best, but still had value as an emblem of the heartbeat of the '66 team and opponents still respected him.
Even after 1970, when Colin was an automatic choice for England, he still missed a fair few games with injuries but it's true that when fit he was an automatic starter both under Ramsey, Mercer (of course) and Revie . Unfortunately due to Norman Hunter's and Shilton's errors, England drew 1-1 v Poland and missed out on qualification to the 1974 World Cup. Of course, the injury in November 1975 brought his international career to an abrupt end. His tally of caps should have been near double what it was.