For me and many others,
Captain America is the penultimate Avenger. Even though he only appeared in the comic series in issue #4, it is hard to think about him not being int he Avengers. He is their leader and battle commander and brings so much to the team. It is interesting that they are launching The Avengers with Captain America in the first film, but it makes sense to have this popular character and vital Avenger along for the first film. It makes sense that they set aside the continuity from the comic in this case as he is so synonymous with the series.