The Theme of Alienation
Contemporary literature did not invent the concept of alienation. Almost all novels, from Daniel Defoe's Robinson Crusoe on, exhibit some degree of alienation. One character may be alienated from another; or a character may be alienated from himself; or he may be alienated from his society, or from nature. Without alienation, in one form or another, there would not be much conflict in novels.
However, in the contemporary novel, alienation of one or all characters from the dominant culture, from the self, from nature, or even from language itself is often the focal theme. The hero or heroine is often an outsider, either accidentally or by design. Often, this alienation is intended in the novel to be a deliberate challenge to American middle-class values.
In novels such as Dorothy Allison's Bastard Out Of Carolina, Toni Morrison's The Bluest Eye, Leslie Marmon Silko's Ceremony, and Joyce Carol Oates's Zombie, for example, the main characters feel completely alone, separated from family, society, and their peers; they even hate themselves. Novels such as Margaret Atwood's Alias Grace, David Guterson's Snow Falling on Cedars, and Peter Hoeg's Smilla's Sense of Snow examine the alienation of those who are social outcasts for one reason or another. Many "immigrant" novels, such as Cynthia Kadohata's The Floating World or Gish Jen's Typical American, explore the effects of alienation from a dominant culture.
However, many (although not all) novels of alienation share a redemptive element, in which the human spirit triumphs despite all the odds against it. In Cold Mountain, for example, one could argue that Inman and Stobrod find ways to atone for their sins and redeem themselves.
Background Information on Jonathan Safran Foer and Everything is Illuminated
For biographical information on Foer, see the Everything Is Illuminated website. It has some good biographical information, but the most illuminating thing there (sorry!) is the author interview. Foer has some great things to say about the novel.