I do not think Charles is necessarily being passes over. I think the analogy of Victoria’s son Edward VII is what Her Majesty is thinking. Like Charles will be advanced, Edward was around 60 when he assumed the throne lived for only another 8 years. I think Her Majesty is already thinking about stepping up William’s “training” a notch since there is a strong possibility that Charles will have a relatively short reign.
I tend to agree with this point of view. Prince William will likely be King one day regardless of whether or not Prince Charles precedes him. Ergo, it hardly seems "unusual" that his grandmother Queen Elizabeth and his father Prince Charles would be grooming him at an early age for his future role as monarch.
Moreover, while I am not a big fan of Prince Charles, if reports I have read are to be believed, there seems to be a great deal of affection between Prince Charles and his sons. William and Harry seem like such nice young men. IMHO, neither one of them appears to be the sort of person who would do anything to disrespect or personally humiliate their father.