There are many advantages to building a site on top of WordPress.  RSS.  Blogging. Calendaring. Simple editing done by authors rather than by a webmaster. Plugins like: ShareThis; Secure Form Mailer; Akismet; Wordpress Automatic Upgrade; and many others. For nonprofits, this means a site can be built and handed over to the organization to update. That as the world moves and plugins develop, your site moves with it.

I have personally struggled a bit trying to decipher how WordPress sites are put together.  The folks at WPDesigner.com put together a great series of articles that instruct users how to create WordPress themes from scratch.  Finally, the veil is lifted.