From IMDb
The title "Magnolia" not only refers to Magnolia Blvd in LA, where much of the movie takes place, but is also similar to the term Charles Fort (who is referenced many places in this movie) coined for a hypothetical region where things that fall from the sky come from - "Magonia".
The page has many other interesting tidbits about the film and its meaning, title included. (Exodus 8:2 and Masonry are alluded to quite often)
Notice that almost every location has a painting or picture of a magnolia.