There's loads of main characters who don't fall into those two categories. Examples:
Harry Potter: Not popular, but has a small group of close friends.
Narnia books: Heroes get sucked into another world, so it doesn't matter how popular they are.
Three Musketeers: Too busy saving Kings to worry about popularity.
Tarzan: Raised by apes, doesn't know much about social graces.
Robinson Crusoe: Stranded on a desert island, not many people to talk to.
Jane Eyre: Works as a Governess in the middle of nowhere, again not many people to talk to.
Alice in Wonderland: Sucked into another world, like Narnia.
Little Women: Consentrates on the relationships between sisters.
Charlotte's Web: ... He's a pig.
Hell, in most of the most famous novels of all time, the characters are too busy doing important stuff to care about popularity, or to brood over how they're better off alone and don't need any friends. Personally I'd just say you're reading the wrong kind of books