If you only know Marvel because of the movies and you'd like to pick up the comic books. This might be a interesting post for you. It might also clear the air for some people who've not been reading comicbooks for that long.
When Marvel started out it was just a guy drawing comics. I can imagine he never dreamt it would ever become this big. At first he created characters and story's. It soon became a succes so there came more characters and more stories. But after years and years of writing at some point you just can't keep on inventing characters. Also at some other point the stories of the really popular characters came at an end so they had to find a solution. This is when they decided to create different universes.
In this post we'll be using Spiderman as an example. Once the first storyline of Spiderman and a great deal of other heroes ended they started over with a new universe. They would take the whole thing back to zero and start over. The character names would stay the same, we'd still be reading about Peter Parker and he would probably still have his spider powers but the main story would change completely. Maybe this time he would not have a girlfriend, or the villains would be way stronger. There are even universes where our heroes are villains!