Using quantifiable measures Wolvie has (at least) had more toys, more comics, more exposure in television and film, and more videogames. As such, more kids would know about him and thus, he would be more popular by my reckoning. On top of all that, Wolvie is almost single-handedly responsible for all the X-fanaticism of the last 25-30 years. The Avengers, though Marvel's "flagship," have never approached being popular at the level of the X-Men since the late 70s, though the new movies may change that.
Cap has always been hanging around as a well known, iconic character. But like Iron Man, no one outside of comic geeks paid all that much attention until the movie came around, while Wolverine was almost constantly available to kids in one cartoon or another, or in movies, or in video games, or in 10 comic titles available at the same time. Cap's recently had exposure due to being on cartoons and the build up to the new film, but that's all in the last year or two.