England boss Roy Hodgson recalled the Manchester United defender for the World Cup double-header against San Marino and Montenegro.
But Ferdinand then pulled out in order to follow a pre-planned fitness routine designed to help him manage his long-standing back problems.
The 34-year-old then compounded the controversy by flying out to Doha to appear as a TV pundit to analyse the San Marino match.
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 says he would not have relished playing San Marino, with current No.1 Joe Hart a virtual spectator in the 8-0 hammering.
"I wouldn't have enjoyed it as a goalkeeper," he said. "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."
England have a much stiffer task against group leaders Montenegro on Tuesday but Shilton is confident they can win.
"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."