A well formed URI is a bonus when it comes to SEO. It helps indexing. Consider that there are sites like PRWeb.com that sell you URI space. Not subdomains, but URI keywords.
Also, while many customers merely want to mouse around, astute web users are impressed with an intuitive URI pattern. If you chop the filename off a path, you should get something logical, like a homepage or an index page, not an error screen.
If your application will eventually be statically cached, you want to able to leverage the file system. So if you have content that will publish well in a static form, I wouldn't hide it behind a convoluted query string.
Also, when conducting web analytics, having an easily parse URI certainly helps you craft your reports.
Your URI doesn't have to correspond to your filesystem. REST style APIs make it quite common to use pathings as a way to divide up areas of their APIs. Your application might leverage some pathing in the URI as a way to separate features. For access control, too: if you want to restrict Googlebot forinstance, it doesn't make a lot of sense to put ?action=blah in a robots.txt file. It does expect paths and fileglobs.
Apache mod_rewrite is awesome. I love it, I live it. I'd rather design in mod_rewrite to proxy a consistent URI space to a changing application codebase early, rather than use mod_rewrite as a bandage on an aging file structure or application layout.