Manchester United defender Ferdinand was recalled for England's World Cup double-header against San Marino and Montenegro, only to pull out in order to follow a pre-planned fitness routine designed to help him manage his long-standing back problems.
Former goalkeeper Shilton, England's record appearance holder with 125 caps, said: "Playing for your country, for me, was the ultimate but that seems to have changed a little bit.
"I don't know the circumstances of what went on but I wanted to get every cap I could. To play in the World Cup and try to win something for England was the ultimate.
"I don't know why Rio isn't playing, whether it's an injury or not, but if he has just pulled out for no reason then I totally disagree with that."
Shilton admitted he would not have enjoyed playing San Marino, where current number one Joe Hart was little more than a spectator as England ran out 8-0 winners.
"I wouldn't have enjoyed it as a goalkeeper," he added. "Those games are a waste of time in a sense, although you have to be on your toes as you don't want to concede against San Marino.
"But it will have been a good confidence booster for the game on Tuesday."
Roy Hodgson's side face a far sterner test against Group H leaders Montenegro on Tuesday night night, but Shilton is confident they can get the job done and take a big step towards qualifying for Brazil.
"I think we are a better team than Montenegro," he said.
"But as we've seen before away from home with a partisan crowd, we've got to be strong mentally, not give anything away defensively, and I'm sure we'll come out with a win because we are the better team. But it's never easy and it's a big match.
"It's a group we should qualify from and if we don't it's not going to look good. We have some good young players coming through and Roy Hodgson is doing a very good job. Hopefully Tuesday will be a springboard for getting to the World Cup."
Double European Cup-winner Shilton, 63, collected the Contribution to League Football award having made more than 1,000 appearances in the Football League.
He said: "This is right up there with any award I've received in my career.
"I never set out to play 1,000 games. You need a bit of luck with injuries, but I just wanted to play football for as long as I possibly could."