The reason for a website receiving a patent is the same reason that any other kind of software program would receive a patent; it provides unique functionality, either in the form of a web application (think Facebook, GMail, salesforce.com, etc.) or some other form of a highly dynamic, interactive website.
Patenting a website would only make sense if it is dynamic/interactive. If the website simply contains static content that does not change and is not interactive, there would be no reason for a patent as copyright protection (and possibly trademark protection, depending on the kind of intellectual property in question) would be sufficient to protect the website's intellectual property.
The first real life example of a patented website that comes to mind is Amazon; it's well known that their one-click ordering process was patented in ~1999. (I think this may have been overturned later after prior art was established, but you get the idea.)
Note: I am not a lawyer. I've just spent a great deal of time researching intellectual property protection during the legal pursuits with my company and my own intellectual property.