Walcott was one of seven players who missed out when coach Fabio Capello trimmed his squad to 23 ahead of the finals which begin in South Africa next week.
Waddle has been a critic of Walcott and said in March that he "doesn't understand the game" and lacks "a football brain".
Reminded of those comments, Waddle told BBC Radio Five Live: "I'll still stand by them.
"He's had a long time at Arsenal, he's playing with fantastic players, a lot of young players around his age group. He's never nailed his shirt at Arsenal.
"I've got nothing against the lad. I just think it's no surprise for me he's not on the plane."
Waddle added: "I look and I just think he doesn't seem to understand the game."