Those transcon routes are where the airlines make their money. At one time (probably still true), if you stay more than 30 days, LAX-JFK (on UA at least) is only avaliable at full fare, which is greater than $2000 round trip. Of course, there are many, many workarounds, but not if you want to fly nonstop.

Another trick for transcons is to use Priceline or Hotwire -- where you'll pay about $200, although you aren't guaranteed nonstops (usually are though) or get to choose times (although you can say no to redeyes if you want).