Led Zeppelin was certainly one of the most misunderstood bands. For one thing, the group was comprised of professional studio musicians. (The photo on the back cover of the first album is more representative of what the members were really like than any other that I've seen. The image that grew around them was more representative of the time and their success than reality.) In listening to their music, one can hear very clearly the professionalism and musicianship that went into the recordings. For an example, listen to the bass lines in "Stairway to Heaven", or to the opening track ("Good Times, Bad Times") on the aforementioned first album: It is one of the most sophisticated studio performances by a hard rock band ever. Compare it with tracks by other bands of the same time and genre, like Blue Cheer, for instance. And this was their starting point, remember.
But like all serious musicians, the band's primary interest became learning and improving. Therefore, experimentation and long passages of improvisation became integral to their work. All four members participated, including Robert Plant, the vocalist. The interplay between Page and Plant became one of the band's innovations. (It could be argued that no other group got so much out of their singer.) Also, their music was based so completely on the blues that some have accused them of plagiarism. (Eliot's line about bad poets imitating as opposed to good poets stealing comes to mind.) But it was a respectful, almost scholarly approach to the blues, not a haphazard one. What resulted from all of this was a group that was never formulaic - their albums and songs display amazing diversity - whose songwriting and studio mastery rivaled anyone's, including The Beatles. As supporting evidence, I recommend giving "The Rain Song" a listen. (To learn more about their music, In the Houses of the Holy: Led Zeppelin and the Power of Rock Music by the musicologist Susan Fast is a must.)