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People are often confused about the differences between WordPress and WordPress.com. WordPress is the free, Open Source web publishing software project, owned by no one individual or company. WordPress.com is a hosted blogging service run by a company called Automattic.
WordPress (sometimes called "WordPress.org" or "self-hosted WordPress" for disambiguation purposes), is software that you can download and install on any web host. It began in 2003 as a fork of b2/cafelog. Licensed by the GPL, you are free to use WordPress without restriction. Sites powered by WordPress may have a "Proudly powered by WordPress" credit, or they may have no credit at all. The absence of any mention of "WordPress.com" is a good indicator that it is a self-hosted WordPress instance).
WordPress.com (a.k.a. "wpcom" or "WP.com") is a for-profit hosted blogging service run by Automattic. WordPress.com launched in 2005, and is the largest WordPress install in the world. It is is powered by WordPress, with some additional plugins and modifications layered on. Having ".wordpress.com" in the domain of the blog or the presence of a "Blog at WordPress.com" promo message or credits image can be used to determine whether a site is hosted at WordPress.com.
What is the overlap between WordPress and WordPress.com? First, Matt Mullenweg is both president of Automattic, and co-founder of WordPress. Matt is involved with both WordPress and WordPress.com. Three of the WordPress lead developers (Ryan Boren, Andrew Ozz, and Peter Westwood) are also Automattic employees. Mark Jaquith is not an Automattic employees and has no involvement with WordPress.com. There are dozens more WordPress core contributors, most of which have no connection with WordPress.com.
Development decisions about WordPress are made without specific regard to their impact on WordPress.com. Any special changes that WordPress.com needs are made on that side, by Automattic employees.
Automattic uses WordPress to power WordPress.com, and it contributes back code and time to the WordPress project. It is a symbiotic relationship. It isn't accurate to say that WordPress is Automattic's product, or that WordPress came from Automattic. Indeed, the opposite is true — Automattic came from WordPress, and Automattic (through WordPress.com) exists as part of the vast WordPress community and ecosystem.
Because it isn't clear what you're talking about — the Open Source project, or the hosted blogging service. They are distinct, and statements about one aren't necessarily true about the other. WordPress.com is its name. You wouldn't call bit.ly, the popular link shortening service, just "bit," would you?
You'll have to ask them. Likely, the downsides of a rebranding campaign would outweigh the benefits. The ambiguity certainly hasn't been all bad. It makes it fairly clear to users that they can migrate their WordPress.com blog to a self-hosted WordPress install.