The 34-year-old Manchester United defender was recalled by manager Roy Hodgson for the fixtures but withdrew in order to follow what has been described as a pre-planned fitness routine.
"Playing for your country, for me, was the ultimate but that seems to have changed a little bit," Shilton told reporters.
|LAMPARD BACKS FERDINAND
|4/1||England are 4/1 with BetVictor to slip to defeat to Montenegro on Tuesday night
"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."
England's current No.1 Joe Hart was little more than a spectator in the 8-0 victory over San Marino, and Shilton admitted he would not have enjoyed playing in that type of game.
"I wouldn't have enjoyed it as a goalkeeper," he continued. "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."
The game on Tuesday is one Shilton expects England to win, although he admits they will have to be wary of Montenegro, especially away from home.
"I think we are a better team than Montenegro," he added. "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."